Alignments for a candidate for asnB in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Bacillus alkalinitrilicus DSM 22532

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_078428617.1 BK574_RS10870 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_002019605.1:WP_078428617.1
          Length = 628

 Score =  640 bits (1650), Expect = 0.0
 Identities = 308/630 (48%), Positives = 439/630 (69%), Gaps = 7/630 (1%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCGFV  F       +  ++E+I+Q  + ++HRGPD +G +HDEHV  GFRRLSI+D++ 
Sbjct: 1   MCGFVSCFEHSK--NSFFRKEIIEQATKKLMHRGPDDEGVYHDEHVSLGFRRLSIVDIDR 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QPLSYE+E YWI+FNGEIYN+ EL++EL   G   +TDSDTEV++A Y    +    K
Sbjct: 59  GKQPLSYENERYWIVFNGEIYNHHELQKELLEVGINLSTDSDTEVIVALYSFIGKGVVHK 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDKEA 180
           LRGMF+FLIW+     L+GARDPFGIKPLY   +   V FAS+ K+L+      ++ + +
Sbjct: 119 LRGMFSFLIWDTEKKKLFGARDPFGIKPLYVVEVETGVGFASDVKALLPLIYQPQVKQSS 178

Query: 181 LQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEEDKLVKE 240
           L+QY++FQ+VP+  T+   V K++PG  F   P   +  + YF   F+P   + ++LV +
Sbjct: 179 LEQYLTFQYVPDTDTMIEGVSKIQPGHYFDWEPGSTLQQREYFHPTFEPKNQDHNELVIK 238

Query: 241 VRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQGFSEVDV 300
           VR  I DSV+ H+RSDV VG FLSGGIDS+ + ++A + + SLKTFSV F + G+SE+DV
Sbjct: 239 VRGTIEDSVSYHLRSDVEVGCFLSGGIDSTIVATLASQQYSSLKTFSVDFNEVGYSEMDV 298

Query: 301 AKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKHVTVAL 360
           A++TAA LG+++    IS EE + ELP I+WH DDP+ADPAAIPLYFV+K A +HV V L
Sbjct: 299 AEKTAAVLGVQHFPYTISAEEVIKELPSIIWHLDDPVADPAAIPLYFVSKLASQHVKVVL 358

Query: 361 SGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGKSLLERGCTPLQ 420
           SGEGADELFGGYNIY+EP++L  F  +   +K+ L+ +  V+PEG++G++ + RGCTPL+
Sbjct: 359 SGEGADELFGGYNIYQEPIALHGFRYLSPNMKRALVQLVRVIPEGVKGRNYMIRGCTPLE 418

Query: 421 DRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVDIHTWMRGD 480
           +RY+GNAKIF    K+++L+H   + +Y+D+TK  +  SS      KMQY+DI TW+RGD
Sbjct: 419 ERYVGNAKIFSNKEKQRVLRHELCS-TYQDITKQLYNNSSKLDSFTKMQYIDIMTWLRGD 477

Query: 481 ILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVL 540
           IL+KADKM+MA+S+ELRVPFLD+ V+++A ++    K     TK +LR+A   ++P HV+
Sbjct: 478 ILVKADKMSMAHSIELRVPFLDREVWNIAKQLSTVEKITKYGTKQILRQAFSPVIPGHVV 537

Query: 541 NRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQLLEDHCADKADNSRKIW 600
           NR+KLGFPVPIR WLKN+  +W ++ I+  + + YI + Y+L LL++H   + D SRK+W
Sbjct: 538 NRRKLGFPVPIRIWLKNQWYDWAKDWIKNDRIEEYIDQQYILDLLDEHALGRKDYSRKLW 597

Query: 601 TVLIFMIWHSINIEKRYMPEELSHQPKEVI 630
           TVL F +W    I   +  E LS + + V+
Sbjct: 598 TVLCFSLW----ITNVFRQENLSKESRSVL 623


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: 1181
Number of extensions: 64
Number of successful extensions: 2
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: 628
Length adjustment: 38
Effective length of query: 594
Effective length of database: 590
Effective search space:   350460
Effective search space used:   350460
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_078428617.1 BK574_RS10870 (asparagine synthase (glutamine-hydrolyzing))
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.24724.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-160  518.9   0.0     1e-159  518.7   0.0    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078428617.1  BK574_RS10870 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078428617.1  BK574_RS10870 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.7   0.0    1e-159    1e-159       1     517 []       2     544 ..       2     544 .. 0.93

  Alignments for each domain:
  == domain 1  score: 518.7 bits;  conditional E-value: 1e-159
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 
                                               Cg+++++++++++  ++e i++ +++l hRGPD+egv++d   e++ lg+rRL+i+d+  g+QPls+e+
  lcl|NCBI__GCF_002019605.1:WP_078428617.1   2 CGFVSCFEHSKNSFFRKEIIEQATKKLMHRGPDDEGVYHD---EHVSLGFRRLSIVDIDRGKQPLSYEN 67 
                                               *********88655599***********************...7************************* PP

                                 TIGR01536  70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137
                                                +++ivfnGEIYNh+eL++el e G+++ t+sDtEVi+a+y   g+ +v++L+GmF f +wd++k++lf
  lcl|NCBI__GCF_002019605.1:WP_078428617.1  68 eRYWIVFNGEIYNHHELQKELLEVGINLSTDSDTEVIVALYSFIGKGVVHKLRGMFSFLIWDTEKKKLF 136
                                               ********************************************************************* PP

                                 TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206
                                                aRD++GikPLY+ + +  + faS +Kall+l   +++++++ l ++lt+q+vp+ +t+ ++v +++p+
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 137 GARDPFGIKPLYVVEVETGVGFASDVKALLPLI-YQPQVKQSSLEQYLTFQYVPDTDTMIEGVSKIQPG 204
                                               ****************999*************9.89********************************* PP

                                 TIGR01536 207 kal..dgeeklee..ywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaai 271
                                               +++  ++  +l++  y++ + e ++++ +elv ++r ++ed+v  +l++dv+vg++lSGG+DS++va++
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 205 HYFdwEPGSTLQQreYFHPTFEPKNQDHNELVIKVRGTIEDSVSYHLRSDVEVGCFLSGGIDSTIVATL 273
                                               ***996666666567****************************************************** PP

                                 TIGR01536 272 akkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairas 340
                                               a+++   ++ktFs++f+ +  ++e ++a+k+a+ lg++h  ++is+eev+kel+ +i++l++p+a++a+
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 274 ASQQYS-SLKTFSVDFN-EVGYSEMDVAEKTAAVLGVQHFPYTISAEEVIKELPSIIWHLDDPVADPAA 340
                                               ****98.8*********.99************************************************* PP

                                 TIGR01536 341 iplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................lpeaselae 393
                                               iply++skla+++ vkVvLsGeGaDElfgGY++++e+ a + ++                +        
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 341 IPLYFVSKLASQH-VKVVLSGEGADELFGGYNIYQEPIALHGFRylspnmkralvqlvrvI-------- 400
                                               *************.*****************************987666666655554441........ PP

                                 TIGR01536 394 kkl....................llqaklakeselkellkakleeelkekeelk.kelkeeseleellr 441
                                                                      + +ak+++++e++++l+++l ++ + ++++  +++++  ++ ++++
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 401 --PegvkgrnymirgctpleeryVGNAKIFSNKEKQRVLRHELCSTYQDITKQLyNNSSKLDSFTKMQY 467
                                               ..0333444445556666666669******************99999887765505555559******* PP

                                 TIGR01536 442 ldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeei 509
                                                d+ ++l++++++k D++smahs+E+RvPflD+e+ ++a ++ +  k+ +  +K +Lr+a+  ++P ++
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 468 IDIMTWLRGDILVKaDKMSMAHSIELRVPFLDREVWNIAKQLSTVEKITKYGTKQILRQAFSPVIPGHV 536
                                               ********************************************************************* PP

                                 TIGR01536 510 leRkKeaf 517
                                               ++R+K +f
  lcl|NCBI__GCF_002019605.1:WP_078428617.1 537 VNRRKLGF 544
                                               *****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (628 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: 13.52
//
[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