Alignments for a candidate for asnB in Methylomicrobium alcaliphilum 20Z

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Methylomicrobium alcaliphilum 20Z

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_014148380.1 MEALZ_RS09330 amidotransferase 1, exosortase A system-associated

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000968535.2:WP_014148380.1
          Length = 627

 Score =  362 bits (928), Expect = e-104
 Identities = 218/625 (34%), Positives = 350/625 (56%), Gaps = 24/625 (3%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG VG+F+     +     EL+ +MN++  HRGPD  G   +  +GFG RRLSIID+ +
Sbjct: 1   MCGIVGIFDLKEKREI--DRELLGRMNEVQFHRGPDEGGLHTEPGLGFGHRRLSIIDLSS 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QP+  +D    + +NGE+YN+ ELR+ELE  GYTF T  DTEV+L  ++ + E    +
Sbjct: 59  GQQPMHSQDGNVVLTYNGEVYNFPELRKELEGLGYTFKTHCDTEVILIGWQAWGESCVDR 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTI-NDQVYFASERKSLMV-AQNDIEIDK 178
           LRGMFAF IW++    L+ ARD  GIKPLYY  + N Q  F SE K+L    Q   E+D 
Sbjct: 119 LRGMFAFAIWDRAKETLFLARDRLGIKPLYYAELPNGQFIFGSELKALKAHPQLPRELDA 178

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFK--TYFKANFKPVQTE-ED 235
            A++ Y  F ++P+P T+  +V K+EPG + TIR  G   F    Y+   F   Q + E 
Sbjct: 179 TAIEDYFGFGYIPDPKTIYKNVHKLEPGFKLTIR-RGQQEFHPVQYWNVEFGVRQVKSEQ 237

Query: 236 KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGFEQQG 294
           +  +E+ +   ++V++ M +DVP+G+FLSGG+DSS +V+ +A      + T S+ F    
Sbjct: 238 ETAEELIERFREAVDIRMVADVPLGAFLSGGVDSSGVVAMMAGLSDQPVNTCSISFGDPA 297

Query: 295 FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKK 354
           F+E   A+  A      +  + + P+++ + + ++   +D+P AD +A+P Y V + AKK
Sbjct: 298 FNESKYAQLVAERYHTAHRVEQVDPDDF-HLIDRLAGLYDEPYADSSALPTYRVCELAKK 356

Query: 355 HVTVALSGEGADELFGGYNIYR-EPLSLKPFERIPSGLKKMLLHV-------AAVMPEGM 406
            VTV LSG+G DE   GY  YR      +    +P GL+K L  +       A   P+  
Sbjct: 357 QVTVVLSGDGGDENLAGYRRYRWHSYEDRMRHILPDGLRKPLFGILGRTYPKADWAPKIF 416

Query: 407 RGKSLLERGCTPLQDRYIGNAKIFEESVKKQL----LKHYNPNLSYRDVTKTYFTESSSY 462
           R KS  E       + Y  +  +    ++  L    LK         +V + +   ++SY
Sbjct: 417 RAKSTFESIARDSLEGYFHSVSVNSNEIRSALFSQNLKQELQGYQAVEVFRRHAKNAASY 476

Query: 463 SDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGT 522
              + +QY+DI T++ GDIL K D+ +MA++LE+RVP LD  + +  + +  +LK K   
Sbjct: 477 DAQSLVQYLDIKTYLPGDILTKVDRASMAHALEVRVPLLDHKLVEWFAGLQPDLKLKGRE 536

Query: 523 TKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVR-NIIQESQTDA-YIHKDY 580
            KY+ +K+ E  +P+ +L R K+GF VP+  W +  + + VR +++ E+ + + Y  + +
Sbjct: 537 GKYIFKKSLENYLPDDILYRSKMGFAVPLASWFRGPLKDRVRESLLGETMSQSGYFDQAF 596

Query: 581 VLQLLEDHCADKADNSRKIWTVLIF 605
           V ++++ H +   DNS  IW++L+F
Sbjct: 597 VKKMVDQHQSGIRDNSTSIWSLLMF 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: 1071
Number of extensions: 56
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: 627
Length adjustment: 38
Effective length of query: 594
Effective length of database: 589
Effective search space:   349866
Effective search space used:   349866
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_014148380.1 MEALZ_RS09330 (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.17957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.7e-158  513.0   0.0   6.5e-158  512.8   0.0    1.0  1  lcl|NCBI__GCF_000968535.2:WP_014148380.1  MEALZ_RS09330 amidotransferase 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000968535.2:WP_014148380.1  MEALZ_RS09330 amidotransferase 1, exosortase A system-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.8   0.0  6.5e-158  6.5e-158       1     517 []       2     561 ..       2     561 .. 0.90

  Alignments for each domain:
  == domain 1  score: 512.8 bits;  conditional E-value: 6.5e-158
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cgi+gi+dlk+k + ++e + +m+e++ hRGPD+ g++ +    + ++ghrRL+iidls+g+QP+++++
  lcl|NCBI__GCF_000968535.2:WP_014148380.1   2 CGIVGIFDLKEKREIDRELLGRMNEVQFHRGPDEGGLHTE---PGLGFGHRRLSIIDLSSGQQPMHSQD 67 
                                               *********99988899*******************9888...7************************* PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                +vv+++nGE+YN+ eLr+ele  Gy+F+t++DtEViL  +++wge +v+rL+GmFAfa+wd++k++lf
  lcl|NCBI__GCF_000968535.2:WP_014148380.1  68 gNVVLTYNGEVYNFPELRKELEGLGYTFKTHCDTEVILIGWQAWGESCVDRLRGMFAFAIWDRAKETLF 136
                                               ********************************************************************* PP

                                 TIGR01536 138 laRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205
                                               laRDrlGikPLYya+  +g+++f+SE+Kal a+++ ++eld++a+ +++++ + p++kt++k+v++lep
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 137 LARDRLGIKPLYYAELpNGQFIFGSELKALKAHPQLPRELDATAIEDYFGFGYIPDPKTIYKNVHKLEP 205
                                               ***************99**************************************************** PP

                                 TIGR01536 206 akal...dgeeklee..ywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268
                                               + +l   +g+++++   yw+ve    + +se+e+ eel e +++av+ r+vadvp+g++lSGG+DSs v
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 206 GFKLtirRGQQEFHPvqYWNVEFGVrQVKSEQETAEELIERFREAVDIRMVADVPLGAFLSGGVDSSGV 274
                                               ***99986777776688*****98757789999************************************ PP

                                 TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337
                                               +a+++  ++++v+t si f  +++++esk+a+ va+   t h+  +++++++ + ++++    +ep a+
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 275 VAMMAGLSDQPVNTCSISFG-DPAFNESKYAQLVAERYHTAHRVEQVDPDDF-HLIDRLAGLYDEPYAD 341
                                               ********************.*****************************97.689************* PP

                                 TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...................... 384
                                               +++ p+y +++la+++ v+VvLsG+G+DE ++GY ++r    e +++                      
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 342 SSALPTYRVCELAKKQ-VTVVLSGDGGDENLAGYRRYRWHSYEDRMRhilpdglrkplfgilgrtypka 409
                                               ****************.***********************99999999*99999999999999998887 PP

                                 TIGR01536 385 ............lpeaselaekkl..........llqaklakeselkellkakleeelkekeelkkelk 431
                                                           +          +          +++ +++++     l++++l++el+  ++++  + 
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 410 dwapkifrakstF----------EsiardslegyFHSVSVNSNEIRSALFSQNLKQELQGYQAVEVFRR 468
                                               7644433322221..........2555566677744444554444444555444444443333222111 PP

                                 TIGR01536 432 ee......seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgke 493
                                               ++       + + +++ld++++l+++++ k Dr+smah lEvRvP+lD++lve  + + p+lkl+  + 
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 469 HAknaasyDAQSLVQYLDIKTYLPGDILTKvDRASMAHALEVRVPLLDHKLVEWFAGLQPDLKLKGREG 537
                                               112234457788899****************************************************** PP

                                 TIGR01536 494 KvlLreaaeellPeeileRkKeaf 517
                                               K+++++ +e++lP++il+R+K++f
  lcl|NCBI__GCF_000968535.2:WP_014148380.1 538 KYIFKKSLENYLPDDILYRSKMGF 561
                                               **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (627 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.33
//
[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