Alignments for a candidate for aceA in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Phyllobacterium endophyticum PEPV15

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_106715487.1 CU100_RS05550 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>NCBI__GCF_003010935.1:WP_106715487.1
          Length = 429

 Score =  551 bits (1419), Expect = e-161
 Identities = 274/410 (66%), Positives = 322/410 (78%), Gaps = 4/410 (0%)

Query: 22  RWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQV 81
           R+  + R YS +DV  L+GSV  ++TLA  GA  LW+ +H+  +VNALGAL+GN A+Q V
Sbjct: 15  RYDGIARPYSPDDVQRLRGSVQIKYTLAENGANRLWKLIHEDGFVNALGALSGNQAMQMV 74

Query: 82  RAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQRADQIAKIEGD- 140
           RAGLKAIYLSGWQVA DAN +   YPDQSLYPAN+ P++ +RIN  LQRADQI   EG  
Sbjct: 75  RAGLKAIYLSGWQVAADANTASAMYPDQSLYPANAAPELAKRINKTLQRADQIETAEGKG 134

Query: 141 TSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLI 200
            SV+ W APIVAD EAGFGG LN +E+ KA I AG AG H+EDQLASEKKCGHLGGKVLI
Sbjct: 135 LSVDTWFAPIVADAEAGFGGPLNAFEIMKAFIEAGAAGVHYEDQLASEKKCGHLGGKVLI 194

Query: 201 PTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPFITGE--RTREGF 258
           PT  HIR L +ARLAADV   PT+VIARTDAEAA L+TSD+DERDQPF+  +  RT EGF
Sbjct: 195 PTAAHIRNLNAARLAADVMGTPTLVIARTDAEAAKLLTSDIDERDQPFVDYDAGRTTEGF 254

Query: 259 YRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQMLAYNCSPSF 318
           Y+ KNG+EPCIARA AYAP+ D+IW ET  PDLE AR+F+E V+ E+P+++LAYNCSPSF
Sbjct: 255 YQVKNGLEPCIARAVAYAPYCDMIWCETSKPDLEQARRFAEGVRKEHPNKLLAYNCSPSF 314

Query: 319 NWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMSAYVELQE 378
           NWKKHLD+ATIA+FQ+EL AMG+KFQFITLAGFH LN+ MF+LA GY   QMSAY ELQE
Sbjct: 315 NWKKHLDEATIARFQRELGAMGYKFQFITLAGFHQLNFGMFELARGYKDRQMSAYSELQE 374

Query: 379 REFAAEERGYTATKHQREVGAGYFDRIATTV-DPNSSTTALTGSTEEGQF 427
            EFAAE  GYTATKHQREVG GYFD ++  +    SSTTA+  STE  QF
Sbjct: 375 AEFAAEVNGYTATKHQREVGTGYFDAVSLAITGGTSSTTAMKESTETAQF 424


Lambda     K      H
   0.316    0.130    0.384 

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: 576
Number of extensions: 22
Number of successful extensions: 4
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: 428
Length of database: 429
Length adjustment: 32
Effective length of query: 396
Effective length of database: 397
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_106715487.1 CU100_RS05550 (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.1754473.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-178  580.4   2.2      1e-97  313.6   0.0    2.0  2  NCBI__GCF_003010935.1:WP_106715487.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106715487.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.6   0.0     1e-97     1e-97      12     252 ..      14     243 ..      10     244 .. 0.97
   2 !  269.5   0.4   2.5e-84   2.5e-84     347     527 .]     242     424 ..     240     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 313.6 bits;  conditional E-value: 1e-97
                             TIGR01346  12 drwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka.ldavy 83 
                                            r+++i r+ys +dv +lrGsv+ + +l++++a++lw++++++    + +++lGal ++q++q+++a l+a+y
  NCBI__GCF_003010935.1:WP_106715487.1  14 GRYDGIARPYSPDDVQRLRGSVQIKYTLAENGANRLWKLIHED----GFVNALGALSGNQAMQMVRAgLKAIY 82 
                                           69*************************************9754....789*********************** PP

                             TIGR01346  84 lsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivad 156
                                           lsGWqv++dan+++ ++Pd+++yPa++ P+  +r++k+l+++d++++ +++  + +         ++ Pivad
  NCBI__GCF_003010935.1:WP_106715487.1  83 LSGWQVAADANTASAMYPDQSLYPANAAPELAKRINKTLQRADQIETAEGKGLSVD--------TWFAPIVAD 147
                                           **********************************************9999877666........5******** PP

                             TIGR01346 157 adaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllv 229
                                           a+aGfGG l++f+++k++ie+Gaagvh+edql+sekkCGhl+Gkvl+p+  h+++l+aarlaadvmg++tl++
  NCBI__GCF_003010935.1:WP_106715487.1 148 AEAGFGGPLNAFEIMKAFIEAGAAGVHYEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLVI 220
                                           ************************************************************************* PP

                             TIGR01346 230 artdaeaatlitsdvdardhefi 252
                                           artdaeaa+l+tsd+d+rd++f+
  NCBI__GCF_003010935.1:WP_106715487.1 221 ARTDAEAAKLLTSDIDERDQPFV 243
                                           *********************97 PP

  == domain 2  score: 269.5 bits;  conditional E-value: 2.5e-84
                             TIGR01346 347 ffdwelertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsf 419
                                           f d++  rt+eGfy+vk+g+e++i+ra a+aPy d++W+ets+Pdle+a++faegv++++P+kllayn+sPsf
  NCBI__GCF_003010935.1:WP_106715487.1 242 FVDYDAGRTTEGFYQVKNGLEPCIARAVAYAPYCDMIWCETSKPDLEQARRFAEGVRKEHPNKLLAYNCSPSF 314
                                           89*********************************************************************** PP

                             TIGR01346 420 nWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdv 489
                                           nW+k+l++ +i++f++elg++GykfqfitlaG+h  ++++f+la+++  + m ay e +q+ e+    +G+++
  NCBI__GCF_003010935.1:WP_106715487.1 315 NWKKHLDEATIARFQRELGAMGYKFQFITLAGFHQLNFGMFELARGYKDRQMSAYSE-LQEAEFaaeVNGYTA 386
                                           ********************************************************9.******9988***** PP

                             TIGR01346 490 lkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                            khq+e+G++yfd +   + gG+s+t+a+++s+e  qf
  NCBI__GCF_003010935.1:WP_106715487.1 387 TKHQREVGTGYFDAVSLAITGGTSSTTAMKESTETAQF 424
                                           ************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (429 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: 15.87
//
[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