Alignments for a candidate for asnB in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Acidithiobacillus ferrooxidans ATCC 23270

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_012607024.1 AFE_RS06345 asparagine synthase (glutamine-hydrolyzing)

Query= CharProtDB::CH_005185
         (632 letters)



>NCBI__GCF_000021485.1:WP_012607024.1
          Length = 632

 Score =  291 bits (745), Expect = 6e-83
 Identities = 201/636 (31%), Positives = 323/636 (50%), Gaps = 46/636 (7%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG VG       +  + +   +     ++V RGPD  G +HD+H   GFRRLSI+D+  
Sbjct: 1   MCGLVGWIG----SDASTRAGAVAYARDLMVSRGPDDAGIWHDDHACMGFRRLSILDLSI 56

Query: 61  GG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAA- 118
            G QP+   D    ++FNGEIYN+ ELR+ LE + YTF + +DTEVLL  YR +  E   
Sbjct: 57  AGHQPMLSVDSRLTLVFNGEIYNFRELRKLLENE-YTFRSHTDTEVLLHGYRAWGWEGLL 115

Query: 119 SKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDK 178
            ++ GMFA  +W+ N   L+ AR  FG KPL+Y   N    FAS  ++L       E+D 
Sbjct: 116 DRIDGMFAIALWDANMQQLHLARHRFGKKPLFYAQTNLGFAFASTLEALRSLAGLNEVDL 175

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDG-DITFKTYFKANFKPVQT-EEDK 236
            A+  ++ +Q VP P T       + P    T   +  D++ + Y+    +P++  +E +
Sbjct: 176 AAVDAFLVYQAVPAPLTFFRGASALLPAHALTYSLETRDLSVERYWDVAVRPLERIDESE 235

Query: 237 LVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQGFS 296
            +  V   +  +V   + +DVPVG+FLSGGIDS  + S+  +   +++T ++GF +  F 
Sbjct: 236 AIDHVDHLLRTAVRRRLIADVPVGAFLSGGIDSGLVTSMMAQ-EGTVETVTLGFAEAAFD 294

Query: 297 EVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKHV 356
           E   A++ AA  G+     V++ E  + +LP+I+     P AD + +    VA  A +H 
Sbjct: 295 ERVYARQVAARWGLRTHETVLNVETLVEQLPRILSQVGQPHADVSLVATDAVAAAAHEHF 354

Query: 357 TVALSGEGADELFGGY-------------NIYREPLSLKPFERIPSG----LKKM--LLH 397
           TV L+G+G DE+FGGY              I   PL    F R P G    ++K+  LL 
Sbjct: 355 TVVLNGDGGDEVFGGYARPVVARAAAQVRRIVPGPLRAT-FRRFPCGGPGPMRKLGLLLR 413

Query: 398 VAAVMPEGMRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFT 457
            A+  PE     ++  RG   ++ +    A  F ++V +      +P+  YR      + 
Sbjct: 414 AASQPPEST---AIYTRGLRGVRAQ--AYAPAFWDTVAQ-----IDPDALYRKA----WA 459

Query: 458 ESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELK 517
                 D  +  Y+D+ T++   +L K D  TMA+SLE R P LD+ + +   ++P  LK
Sbjct: 460 HLDQAEDAERALYLDLTTYLPDQLLSKMDTATMAHSLEARSPLLDRALVEFGMRLPITLK 519

Query: 518 TKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNII--QESQTDAY 575
            K+  TKYLL++ AE  +P  V+ R+K GF +P+  WL+  +  +V      Q   +  +
Sbjct: 520 LKHYRTKYLLKRLAERYLPHDVIYRRKQGFVIPLAAWLRGRLLPYVEAAFRHQSFVSREW 579

Query: 576 IHKDYVLQLLEDHCADKADNSRKIWTVLIFMIWHSI 611
           +  D++ +LL    A     +  +WTV +  IW ++
Sbjct: 580 LLADFLSELLTRFKAGDDAVAGTLWTVFVLAIWAAL 615


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: 875
Number of extensions: 42
Number of successful extensions: 8
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: 632
Length adjustment: 38
Effective length of query: 594
Effective length of database: 594
Effective search space:   352836
Effective search space used:   352836
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_012607024.1 AFE_RS06345 (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.28941.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-132  427.2   0.0   6.7e-132  427.0   0.0    1.0  1  lcl|NCBI__GCF_000021485.1:WP_012607024.1  AFE_RS06345 asparagine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021485.1:WP_012607024.1  AFE_RS06345 asparagine synthase (glutamine-hydrolyzing)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.0   0.0  6.7e-132  6.7e-132       1     517 []       2     549 ..       2     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 427.0 bits;  conditional E-value: 6.7e-132
                                 TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 
                                               Cg++g++ ++a ++    a++   +++  RGPD+ g+w+d   ++a++g+rRL+i dls + +QP+ + 
  lcl|NCBI__GCF_000021485.1:WP_012607024.1   2 CGLVGWIGSDASTRA--GAVAYARDLMVSRGPDDAGIWHD---DHACMGFRRLSILDLSIAgHQPMLSV 65 
                                               *********876555..55666679***************...8***************888****999 PP

                                 TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkge 135
                                               + + ++vfnGEIYN++eLr+ le++ y+F++++DtEV+L+ y++wg e l++r++GmFA+alwd++ ++
  lcl|NCBI__GCF_000021485.1:WP_012607024.1  66 DsRLTLVFNGEIYNFRELRKLLENE-YTFRSHTDTEVLLHGYRAWGwEGLLDRIDGMFAIALWDANMQQ 133
                                               98*****************999999.******************************************* PP

                                 TIGR01536 136 lflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkele 204
                                               l+laR r+G+kPL+ya+++  ++faS + al +l    +e+d +a+  +l +q vp + t+f++   l 
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 134 LHLARHRFGKKPLFYAQTNLGFAFASTLEALRSLAG-LNEVDLAAVDAFLVYQAVPAPLTFFRGASALL 201
                                               **********************************94.6799**************************** PP

                                 TIGR01536 205 pakal.....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSsl 267
                                               pa+al     + + ++e+yw+v+++   + +e+e+++++++ll+ av++rl+advpvg++lSGG+DS l
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 202 PAHALtysleTRDLSVERYWDVAVRPlERIDESEAIDHVDHLLRTAVRRRLIADVPVGAFLSGGIDSGL 270
                                               *****9887666667777*****9986888999************************************ PP

                                 TIGR01536 268 vaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleepta 336
                                               v++++++e    v+t ++gf+ ++++de  +ar+va+  g++ +e++++ e+++++l++++ ++ +p a
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 271 VTSMMAQEGT--VETVTLGFA-EAAFDERVYARQVAARWGLRTHETVLNVETLVEQLPRILSQVGQPHA 336
                                               *******955..*********.*********************************************** PP

                                 TIGR01536 337 irasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale..................... 384
                                               + + + + +++ +a+e+ ++VvL G+G+DE+fgGY++   a a+++++                     
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 337 DVSLVATDAVAAAAHEH-FTVVLNGDGGDEVFGGYARPVVARAAAQVRrivpgplratfrrfpcggpgp 404
                                               *****************.**********************99999999999999999999988888888 PP

                                 TIGR01536 385 .......lpeaselaekkl...llqaklakeselkellkakleeelkek.eelkkelkeeseleellrl 442
                                                      l  as+  e++    +  + ++++     ++ +  + +     ++  ++l ++++ e++l+l
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 405 mrklgllLRAASQPPESTAiytRGLRGVRAQAYAPAFWDTVAQIDPDALyRKAWAHLDQAEDAERALYL 473
                                               88877753333344444442223333333333333333333333322220222333444499******* PP

                                 TIGR01536 443 dlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeil 510
                                               dl+++l+d l+ k D ++mahslE+R P+lD++lve+ +++p  lkl++ ++K+lL+++ae++lP+++ 
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 474 DLTTYLPDQLLSKmDTATMAHSLEARSPLLDRALVEFGMRLPITLKLKHYRTKYLLKRLAERYLPHDVI 542
                                               ********************************************************************* PP

                                 TIGR01536 511 eRkKeaf 517
                                               +R+K++f
  lcl|NCBI__GCF_000021485.1:WP_012607024.1 543 YRRKQGF 549
                                               *****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (632 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: 00:00:00.03
# Mc/sec: 8.47
//
[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