Alignments for a candidate for aceA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Azospirillum brasilense Sp245

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AZOBR_RS02405 AZOBR_RS02405 isocitrate lyase

Query= BRENDA::A0A3S5YB92
         (429 letters)



>FitnessBrowser__azobra:AZOBR_RS02405
          Length = 425

 Score =  545 bits (1405), Expect = e-160
 Identities = 275/413 (66%), Positives = 325/413 (78%), Gaps = 7/413 (1%)

Query: 22  RWKGVTRNYTAEQVVKLQGTVVEEATLARRGSEILWDLVNNEDYINSLGALTGNQAVQQV 81
           R++G+ R+YT + V +L G+V  E TLA  G++ LW+L+N E YIN+LGALTGNQA+Q V
Sbjct: 15  RFEGIKRDYTQDDVKRLSGSVKIEYTLAEMGAQRLWELLNTEPYINTLGALTGNQAMQAV 74

Query: 82  RAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALLRADEIAKVEGDT 141
           +AGLKAIYLSGWQVAGDANL+G  YPDQSLYPANSVP VV RINN   RADEI   EG  
Sbjct: 75  KAGLKAIYLSGWQVAGDANLAGQMYPDQSLYPANSVPAVVERINNTFKRADEIQTAEGKG 134

Query: 142 SVDNWLAPIVADGEAGFGGALNVYELQKAMIAAGVAGSHWEDQLASEKKCGHLGGKVLIP 201
               W API+AD EAGFGG LNV+EL KAMI AG +G H+EDQLASEKKCGHLGGKVLIP
Sbjct: 135 DT-YWFAPIIADAEAGFGGPLNVFELMKAMIKAGASGVHFEDQLASEKKCGHLGGKVLIP 193

Query: 202 TQQHIRTLTSARLAADVADVPTVVIARTDAEAATLLTSDVDERDREFLD--GTRTAEGFY 259
           TQQHIRTL +ARLAAD     T+V+ RTDAE+A L+TSDVDERD  F+D    RT+EGF+
Sbjct: 194 TQQHIRTLNAARLAADTMGTSTIVLCRTDAESAQLITSDVDERDHPFIDFDAGRTSEGFF 253

Query: 260 GVKNG--IEPCIARAKAYAPYSDLIWMETGVPDLEVAKKFAEAVRSEFPDQLLAYNCSPS 317
            +K G  ++ CIAR  +YAPYSDL+W ET  P+LE AK+FAEA+R EFP++LLAYNCSPS
Sbjct: 254 RLKKGTGVDHCIARGLSYAPYSDLLWWETSRPNLEEAKRFAEAIRKEFPNKLLAYNCSPS 313

Query: 318 FNWKAHLDDATIAKFQKELGAMGFKFQFITLAGFHSLNYGMFDLAHGYAREGMTAFVDLQ 377
           FNWKA+LD+A IAKFQ+E+GAMG+KFQF+TLAGFHSLNY  F LA GYA  GM A+ +LQ
Sbjct: 314 FNWKANLDEADIAKFQREIGAMGYKFQFVTLAGFHSLNYSAFKLAKGYAARGMAAYSELQ 373

Query: 378 EREFKAAEERGFTAIKHQREVGAGYFDSIATTVD-PNTSTAALKGSTEEGQFH 429
           E EF AAE  G+TA KHQREVG GYFD++AT +    +ST A K STE  QFH
Sbjct: 374 EAEF-AAEAEGYTATKHQREVGTGYFDAVATAISGGQSSTTAYKDSTEADQFH 425


Lambda     K      H
   0.316    0.132    0.388 

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: 598
Number of extensions: 21
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: 429
Length of database: 425
Length adjustment: 32
Effective length of query: 397
Effective length of database: 393
Effective search space:   156021
Effective search space used:   156021
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS02405 AZOBR_RS02405 (isocitrate lyase)
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))

# 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/TIGR01346.hmm
# target sequence database:        /tmp/gapView.13188.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01346  [M=527]
Accession:   TIGR01346
Description: isocit_lyase: isocitrate lyase
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-178  579.1   2.9   1.9e-101  325.9   0.0    2.0  2  lcl|FitnessBrowser__azobra:AZOBR_RS02405  AZOBR_RS02405 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS02405  AZOBR_RS02405 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.9   0.0  1.9e-101  1.9e-101      11     252 ..      13     241 ..       4     242 .. 0.96
   2 !  256.2   0.8   2.7e-80   2.7e-80     347     527 .]     240     424 ..     240     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 325.9 bits;  conditional E-value: 1.9e-101
                                 TIGR01346  11 ddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka. 78 
                                                 r+e+ikrdy+ +dv +l Gsv+ e +l++++a++lw++l++e     +++tlGal+++q++q +ka 
  lcl|FitnessBrowser__azobra:AZOBR_RS02405  13 AARFEGIKRDYTQDDVKRLSGSVKIEYTLAEMGAQRLWELLNTE----PYINTLGALTGNQAMQAVKAg 77 
                                               579**************************************987....57******************* PP

                                 TIGR01346  79 ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyi 147
                                               l+a+ylsGWqv++danl+++++Pd+++yPa++vP++ver++++++++d++q+ +++   d         
  lcl|FitnessBrowser__azobra:AZOBR_RS02405  78 LKAIYLSGWQVAGDANLAGQMYPDQSLYPANSVPAVVERINNTFKRADEIQTAEGKG--DT-------- 136
                                               ***************************************************988753..33........ PP

                                 TIGR01346 148 dylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaar 216
                                                ++ Pi+ada+aGfGG l+vf+l+k++i++Ga+gvh+edql+sekkCGhl+Gkvl+p+q+h+++l+aar
  lcl|FitnessBrowser__azobra:AZOBR_RS02405 137 YWFAPIIADAEAGFGGPLNVFELMKAMIKAGASGVHFEDQLASEKKCGHLGGKVLIPTQQHIRTLNAAR 205
                                               49******************************************************************* PP

                                 TIGR01346 217 laadvmgvetllvartdaeaatlitsdvdardhefi 252
                                               laad mg+ t+++ rtdae+a+litsdvd+rdh+fi
  lcl|FitnessBrowser__azobra:AZOBR_RS02405 206 LAADTMGTSTIVLCRTDAESAQLITSDVDERDHPFI 241
                                               ***********************************9 PP

  == domain 2  score: 256.2 bits;  conditional E-value: 2.7e-80
                                 TIGR01346 347 ffdwelertreGfyrvkg..gveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllay 413
                                               f d++  rt+eGf+r+k   gv+ +i+r+ ++aPy+dl+W ets P+leeak+fae+++++fP+kllay
  lcl|FitnessBrowser__azobra:AZOBR_RS02405 240 FIDFDAGRTSEGFFRLKKgtGVDHCIARGLSYAPYSDLLWWETSRPNLEEAKRFAEAIRKEFPNKLLAY 308
                                               78**************9622689********************************************** PP

                                 TIGR01346 414 nlsPsfnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqre 482
                                               n+sPsfnW+++l++ +i+kf++e+g++Gykfqf+tlaG+hs +++ f+lak++a +Gm ay e +q+ e
  lcl|FitnessBrowser__azobra:AZOBR_RS02405 309 NCSPSFNWKANLDEADIAKFQREIGAMGYKFQFVTLAGFHSLNYSAFKLAKGYAARGMAAYSE-LQEAE 376
                                               **************************************************************9.***** PP

                                 TIGR01346 483 l...edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               +    +G+++ khq+e+G++yfd +++ + gG s+t+a + s+e dqf
  lcl|FitnessBrowser__azobra:AZOBR_RS02405 377 FaaeAEGYTATKHQREVGTGYFDAVATAISGGQSSTTAYKDSTEADQF 424
                                               *99999*****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (425 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.66
//
[ok]

This GapMind analysis is from Apr 09 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