Alignments for a candidate for aceA in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Amycolatopsis halophila YIM 93223

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_034273644.1 AMYHA_RS20455 isocitrate lyase

Query= BRENDA::A0A3S5YB92
         (429 letters)



>NCBI__GCF_000504245.1:WP_034273644.1
          Length = 428

 Score =  676 bits (1744), Expect = 0.0
 Identities = 324/427 (75%), Positives = 378/427 (88%), Gaps = 2/427 (0%)

Query: 2   STTGTPRTAEEIQKDWDTNPRWKGVTRNYTAEQVVKLQGTVVEEATLARRGSEILWDLVN 61
           +T    + A E+ K+W+TNPRWKG+ R+YTAE VVKL+G+V+EE TLARRG+E LWDL++
Sbjct: 4   TTKSREQAAAELAKEWETNPRWKGIDRSYTAEDVVKLRGSVIEENTLARRGAEKLWDLLH 63

Query: 62  NEDYINSLGALTGNQAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVV 121
            EDY+++LGALTG QAVQQVRAGLKAIYLSGWQVA DANL+G TYPDQSLYPANSVP VV
Sbjct: 64  TEDYVHALGALTGGQAVQQVRAGLKAIYLSGWQVAADANLAGQTYPDQSLYPANSVPAVV 123

Query: 122 RRINNALLRADEIAKVEGDTSVDNWLAPIVADGEAGFGGALNVYELQKAMIAAGVAGSHW 181
           RRINNAL RAD+I   EG+T +D W APIVAD EAGFGG LN +EL K MIAAG AG HW
Sbjct: 124 RRINNALGRADQINYAEGNTDID-WYAPIVADAEAGFGGPLNAFELMKGMIAAGAAGVHW 182

Query: 182 EDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLLTSDV 241
           EDQLASEKKCGHLGGKVL+PT+QH+RTL +ARLA+DV+DVP++VIARTDAEAATL+TSDV
Sbjct: 183 EDQLASEKKCGHLGGKVLVPTKQHVRTLNAARLASDVSDVPSIVIARTDAEAATLMTSDV 242

Query: 242 DERDREFLDGTRTAEGFYGVKNGIEPCIARAKAYAPYSDLIWMETGVPDLEVAKKFAEAV 301
           DERD +FL G RT+EGFY V+NGIEPCI RAKAYAPYSDLIWMETG PDLEVA++FAEAV
Sbjct: 243 DERDEKFLTGERTSEGFYKVRNGIEPCIERAKAYAPYSDLIWMETGTPDLEVARQFAEAV 302

Query: 302 RSEFPDQLLAYNCSPSFNWKAHLDDATIAKFQKELGAMGFKFQFITLAGFHSLNYGMFDL 361
           ++EFPDQ+LAYNCSPSFNW+ +LDDATIAKFQ+ELG MG+KFQFITLAGFH+LNY MFDL
Sbjct: 303 KAEFPDQMLAYNCSPSFNWRKNLDDATIAKFQRELGHMGYKFQFITLAGFHALNYSMFDL 362

Query: 362 AHGYAREGMTAFVDLQEREFKAAEERGFTAIKHQREVGAGYFDSIATTVDPNTSTAALKG 421
           A+GYAREGMTA+VDLQ+REF A+EERGFTA+KHQRE G G+FD ++T ++P +ST AL G
Sbjct: 363 AYGYAREGMTAYVDLQDREF-ASEERGFTAVKHQREAGTGWFDLVSTAINPESSTTALTG 421

Query: 422 STEEGQF 428
           STEE QF
Sbjct: 422 STEEAQF 428


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: 703
Number of extensions: 20
Number of successful extensions: 3
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: 428
Length adjustment: 32
Effective length of query: 397
Effective length of database: 396
Effective search space:   157212
Effective search space used:   157212
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 WP_034273644.1 AMYHA_RS20455 (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.1376470.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-195  636.1   3.9   9.6e-111  356.6   0.2    2.0  2  NCBI__GCF_000504245.1:WP_034273644.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034273644.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.6   0.2  9.6e-111  9.6e-111       2     254 ..      13     252 ..      12     253 .. 0.97
   2 !  281.6   0.3   5.2e-88   5.2e-88     353     527 .]     253     428 .]     252     428 .] 0.99

  Alignments for each domain:
  == domain 1  score: 356.6 bits;  conditional E-value: 9.6e-111
                             TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsq 74 
                                           +e+ keW+t++rw++i r y+a+dvvklrGsv+ee++l++++a+klw++l++e+    ++++lGal+++q++q
  NCBI__GCF_000504245.1:WP_034273644.1  13 AELAKEWETNPRWKGIDRSYTAEDVVKLRGSVIEENTLARRGAEKLWDLLHTED----YVHALGALTGGQAVQ 81 
                                           799***********************************************9875....69************* PP

                             TIGR01346  75 qaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkely 146
                                           q++a l+a+ylsGWqv++danl+++++Pd+++yPa++vP++v+r+++al ++d+++  ++++           
  NCBI__GCF_000504245.1:WP_034273644.1  82 QVRAgLKAIYLSGWQVAADANLAGQTYPDQSLYPANSVPAVVRRINNALGRADQINYAEGNT----------D 144
                                           *******************************************************9987743..........4 PP

                             TIGR01346 147 idylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaa 219
                                           id+  Pivada+aGfGG l++f+l+k +i++Gaagvh+edql+sekkCGhl+Gkvlvp+++hv++l+aarla 
  NCBI__GCF_000504245.1:WP_034273644.1 145 IDWYAPIVADAEAGFGGPLNAFELMKGMIAAGAAGVHWEDQLASEKKCGHLGGKVLVPTKQHVRTLNAARLAS 217
                                           9************************************************************************ PP

                             TIGR01346 220 dvmgvetllvartdaeaatlitsdvdardhefivG 254
                                           dv +v+ +++artdaeaatl+tsdvd+rd++f++G
  NCBI__GCF_000504245.1:WP_034273644.1 218 DVSDVPSIVIARTDAEAATLMTSDVDERDEKFLTG 252
                                           **********************************9 PP

  == domain 2  score: 281.6 bits;  conditional E-value: 5.2e-88
                             TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkal 425
                                           ert+eGfy+v++g+e++i raka+aPy+dl+Wmet+tPdle a++fae+vk++fPd++layn+sPsfnW k+l
  NCBI__GCF_000504245.1:WP_034273644.1 253 ERTSEGFYKVRNGIEPCIERAKAYAPYSDLIWMETGTPDLEVARQFAEAVKAEFPDQMLAYNCSPSFNWRKNL 325
                                           8************************************************************************ PP

                             TIGR01346 426 eddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdvlkhqke 495
                                           +d +i+kf++elg++GykfqfitlaG+h+ ++++fdla+++a+eGm+ayv+ +q re+   e+G++++khq+e
  NCBI__GCF_000504245.1:WP_034273644.1 326 DDATIAKFQRELGHMGYKFQFITLAGFHALNYSMFDLAYGYAREGMTAYVD-LQDREFaseERGFTAVKHQRE 397
                                           ***************************************************.*******999*********** PP

                             TIGR01346 496 sGaeyfdqllklvqgGvsataalaksveedqf 527
                                           +G+++fd + + +++  s+t+al++s+ee qf
  NCBI__GCF_000504245.1:WP_034273644.1 398 AGTGWFDLVSTAINP-ESSTTALTGSTEEAQF 428
                                           ***************.9**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (428 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.58
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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