Alignments for a candidate for asnB in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sedimenticola selenatireducens DSM 17993

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_029132462.1 A3GO_RS0104955 amidotransferase 1, exosortase A system-associated

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000428045.1:WP_029132462.1
          Length = 635

 Score =  370 bits (951), Expect = e-107
 Identities = 230/629 (36%), Positives = 350/629 (55%), Gaps = 32/629 (5%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG VG+F+     + +D   L+ +MNQ  VHRGPD  G   +  VG G RRLSIID+ +
Sbjct: 1   MCGIVGIFDTTGQREISDS--LLSRMNQTQVHRGPDEQGIHIEPGVGLGHRRLSIIDLAS 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QPL  ED +  + +NGEIYN+ EL  EL++KG+ F T SDTEV++  +  + E     
Sbjct: 59  GQQPLFNEDHSVVVTYNGEIYNFPELSSELKSKGHLFRTHSDTEVIVHAWEEWGESCVEH 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVY-FASERKSLMV-AQNDIEIDK 178
            RGMFAF +W++N   L+ ARD  GIKPL+Y  ++D  + F SE KSL V  +   EID 
Sbjct: 119 FRGMFAFAVWDRNQETLFLARDRLGIKPLFYAQLDDGFFIFGSELKSLKVDPRLGREIDP 178

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITF--KTYFKANFKP--VQTEE 234
            A+++Y +F ++PEP T+   V K+ PG   T+R  G IT   K Y+  +FKP    TE+
Sbjct: 179 AAVEEYFTFGYIPEPRTIYRKVHKLSPGHSLTLR-KGQITAAPKQYWDVSFKPHAAMTEQ 237

Query: 235 D---KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGF 290
           D   +L++ +R+A    V++ M ++VP+G+FLSGG+DSS +V  +A      + T S+ F
Sbjct: 238 DAGNELIERLREA----VDIRMIAEVPLGAFLSGGVDSSAVVGLMAGLSEKPVNTCSISF 293

Query: 291 EQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAK 350
               F+E   A++ A     ++  + + P+++ + +  +   +D+P AD +A+P Y V +
Sbjct: 294 GDPKFNESAYAEKVARRFSTDHRVEQVDPDDF-DLIDHLADLYDEPYADSSALPTYRVCQ 352

Query: 351 EAKKHVTVALSGEGADELFGGYNIY-------REPLSLKPFERIP-SGLKKMLLHVAAVM 402
            AK+ VTV LSG+G DE   GY  Y       R    L P  R P  G    L   A   
Sbjct: 353 LAKQQVTVVLSGDGGDENLAGYRRYRWHTYEERMRAMLPPAIRQPLFGTLGRLYPKADWA 412

Query: 403 PEGMRGKSLLERGCTPLQDRYIGNAKIFEESVKKQL----LKHYNPNLSYRDVTKTYFTE 458
           P   R KS  E         Y+ +  I    ++ QL    LK         +V + +  +
Sbjct: 413 PRVFRAKSTFESMARDTLQGYMHSVSILSNQMRDQLFSDKLKRELQGYQAIEVFRRHAGQ 472

Query: 459 SSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKT 518
           + +   ++ +QY+D+ T++ GDIL K D+ +MA+SLE+RVP LD  + D  S +P E+K 
Sbjct: 473 APTDHPLSLVQYLDLKTYLVGDILTKVDRASMAHSLEVRVPLLDHHLVDWISGLPPEMKL 532

Query: 519 KNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRN--IIQESQTDAYI 576
           +    KYL +KA E ++P  +L RKK+GF VP+  W +  + + VRN  +  E       
Sbjct: 533 RGSEGKYLFKKALEPMLPHDILYRKKMGFAVPLASWFRGPLRDKVRNSLLSDEMLGSGLF 592

Query: 577 HKDYVLQLLEDHCADKADNSRKIWTVLIF 605
           ++ Y+  L++ H +   D S  IWT+L+F
Sbjct: 593 NERYLHTLVDHHQSGIRDYSASIWTLLMF 621


Lambda     K      H
   0.319    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1034
Number of extensions: 48
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 632
Length of database: 635
Length adjustment: 38
Effective length of query: 594
Effective length of database: 597
Effective search space:   354618
Effective search space used:   354618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate WP_029132462.1 A3GO_RS0104955 (amidotransferase 1, exosortase A system-associated)
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01536.hmm
# target sequence database:        /tmp/gapView.6625.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-157  510.4   0.0   4.1e-157  510.2   0.0    1.0  1  lcl|NCBI__GCF_000428045.1:WP_029132462.1  A3GO_RS0104955 amidotransferase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029132462.1  A3GO_RS0104955 amidotransferase 1, exosortase A system-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.2   0.0  4.1e-157  4.1e-157       1     517 []       2     561 ..       2     561 .. 0.91

  Alignments for each domain:
  == domain 1  score: 510.2 bits;  conditional E-value: 4.1e-157
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgi+gi+d + + + + + +++m++t+ hRGPD++g++++    +++lghrRL+iidl +g+QPl ne+
  lcl|NCBI__GCF_000428045.1:WP_029132462.1   2 CGIVGIFDTTGQREISDSLLSRMNQTQVHRGPDEQGIHIE---PGVGLGHRRLSIIDLASGQQPLFNED 67 
                                               *********99987799********************999...7************************* PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                +vv+++nGEIYN+ eL  el+ kG+ F+t+sDtEVi++a+eewge +ve+++GmFAfa+wd+++++lf
  lcl|NCBI__GCF_000428045.1:WP_029132462.1  68 hSVVVTYNGEIYNFPELSSELKSKGHLFRTHSDTEVIVHAWEEWGESCVEHFRGMFAFAVWDRNQETLF 136
                                               999****************************************************************** PP

                                 TIGR01536 138 laRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205
                                               laRDrlGikPL+ya+  +g ++f+SE+K+l   ++  +e+d +a+ e++t+ + p+++t++++v++l+p
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 137 LARDRLGIKPLFYAQLdDGFFIFGSELKSLKVDPRLGREIDPAAVEEYFTFGYIPEPRTIYRKVHKLSP 205
                                               **************98799************************************************** PP

                                 TIGR01536 206 akal.....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268
                                               +++l     + +++ ++yw+v+ +   +++e+++ +el e l++av+ r++a+vp+g++lSGG+DSs+v
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 206 GHSLtlrkgQITAAPKQYWDVSFKPhAAMTEQDAGNELIERLREAVDIRMIAEVPLGAFLSGGVDSSAV 274
                                               ****9885555555666*****998567889999*********************************** PP

                                 TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                               + +++  ++++v+t si f  +++++es++a+kva+ + t+h+  +++++++ + ++++    +ep a+
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 275 VGLMAGLSEKPVNTCSISFG-DPKFNESAYAEKVARRFSTDHRVEQVDPDDF-DLIDHLADLYDEPYAD 341
                                               ********************.****************************995.899************* PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...................... 384
                                               +++ p+y +++la+++ v+VvLsG+G+DE ++GY ++r  + ee+++                      
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 342 SSALPTYRVCQLAKQQ-VTVVLSGDGGDENLAGYRRYRWHTYEERMRamlppairqplfgtlgrlypka 409
                                               ****************.******************************9*99999999999999998887 PP

                                 TIGR01536 385 ............lpeaselaekkl..........llqaklakeselkellkakleeelkekeelkkelk 431
                                                           +          +          +++ ++ +++   +l++ kl++el+  ++ +  + 
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 410 dwaprvfrakstF----------EsmardtlqgyMHSVSILSNQMRDQLFSDKLKRELQGYQAIEVFRR 468
                                               7755554444433..........1334444555577777777777777777777666654443322222 PP

                                 TIGR01536 432 ee......seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgke 493
                                               ++      + l+ +++ldl+++l ++++ k Dr+smahslEvRvP+lD++lv+ +  +ppe+klr  + 
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 469 HAgqaptdHPLSLVQYLDLKTYLVGDILTKvDRASMAHSLEVRVPLLDHHLVDWISGLPPEMKLRGSEG 537
                                               2233455499*********************************************************** PP

                                 TIGR01536 494 KvlLreaaeellPeeileRkKeaf 517
                                               K+l+++a+e +lP++il+RkK++f
  lcl|NCBI__GCF_000428045.1:WP_029132462.1 538 KYLFKKALEPMLPHDILYRKKMGF 561
                                               **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (635 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.55
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis