Alignments for a candidate for aceA in Methyloferula stellata AR4 AR4T

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Methyloferula stellata AR4 AR4T

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_020173599.1 A3OQ_RS0101600 isocitrate lyase

Query= BRENDA::Q8RPZ0
         (436 letters)



>NCBI__GCF_000385335.1:WP_020173599.1
          Length = 438

 Score =  516 bits (1329), Expect = e-151
 Identities = 263/411 (63%), Positives = 320/411 (77%), Gaps = 7/411 (1%)

Query: 30  RWRDIERTYGAEEVIRLSGSVREEHTLARRGADRLWRQLHELDYVHALGALTGGQAVQQV 89
           R+  I R YG EEV RL GS    +TLA R A++LW+ + E  YVH+LGA+TG QA+Q  
Sbjct: 18  RFDGIRRPYGPEEVKRLRGSFPIAYTLAERSANKLWKLMQERPYVHSLGAVTGNQAMQMA 77

Query: 90  RAGLQAIYLFGWQVAADANQAGHTYPDQSLYPANSVPQVVRRINNALLRADQIATAENAG 149
           RAGL+AIYL GWQVAADAN AG  YPDQSLYPANS P++ R+IN    R D+I  AE  G
Sbjct: 78  RAGLEAIYLSGWQVAADANVAGAMYPDQSLYPANSGPELARKINKTFKRVDEIEHAE--G 135

Query: 150 DGT-DWLAPIVADAEAGFGGPLNAFELTKAMIEAGAAGIHYEDQLASEKKCGHLGGKVLV 208
           + T DW  PI+ADAEAGFGGPLN FE+ KA IEAG A +H+EDQLASEKKCGHLGGKVL+
Sbjct: 136 NVTRDWFLPIIADAEAGFGGPLNVFEIMKAYIEAGVAAVHFEDQLASEKKCGHLGGKVLL 195

Query: 209 PTAQHIRTLNAARLAADIADVPTVIIARTDALAASLITSDVDERDAEFLTGE-RTAEGFH 267
           PTAQH R+L+AARLAAD+  VPT+++ARTDA +A LITSDVDERD  F+  + RT EGF+
Sbjct: 196 PTAQHERSLSAARLAADVMGVPTLVVARTDAESAKLITSDVDERDRPFIIPDSRTPEGFY 255

Query: 268 RVRNG--MAPVIARGLAYAPYADLLWMETGTPDLAQAREFAEAIHAQYPEQLLAYNCSPS 325
           R+++G  +A  I+RGLAYA  +D+LW ET  PDL +AREFAEA+H ++P +LLAYNCSPS
Sbjct: 256 RLKDGTGLAHCISRGLAYAEVSDMLWWETSHPDLGEAREFAEAVHKKFPGKLLAYNCSPS 315

Query: 326 FNWRAALDDDRIAKFQRELGAMGYRFQFITLAGFHSLNHAMFDLARGYAEHGMTAYVDLQ 385
           FNWRA LD   I KFQRELGAMGY++QF+TLAGFHSLN +M++LA GY + GM AY +LQ
Sbjct: 316 FNWRAKLDKATIEKFQRELGAMGYKYQFVTLAGFHSLNLSMYELALGYKDRGMDAYSELQ 375

Query: 386 EREFAAQADGFTAVRHQREVGTGYFDLVSTAVN-PASSTTALSGSTEEEQF 435
           + EF  +A G++A RHQREVGTGYFD VS A++  ASSTTA+  STE  QF
Sbjct: 376 QAEFDLEAKGYSATRHQREVGTGYFDAVSVAISGGASSTTAMGESTESAQF 426


Lambda     K      H
   0.318    0.131    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: 569
Number of extensions: 16
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: 436
Length of database: 438
Length adjustment: 32
Effective length of query: 404
Effective length of database: 406
Effective search space:   164024
Effective search space used:   164024
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_020173599.1 A3OQ_RS0101600 (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.1810776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.8e-165  536.2   0.1    2.6e-93  299.1   0.0    2.0  2  NCBI__GCF_000385335.1:WP_020173599.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000385335.1:WP_020173599.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.1   0.0   2.6e-93   2.6e-93      12     253 ..      17     245 ..      13     249 .. 0.96
   2 !  235.4   0.2   5.2e-74   5.2e-74     353     527 .]     248     426 ..     246     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: 299.1 bits;  conditional E-value: 2.6e-93
                             TIGR01346  12 drwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka.ldavy 83 
                                            r+++i+r+y  ++v +lrGs++   +l+++ a+klw+++++    + ++++lGa++++q++q+a+a l+a+y
  NCBI__GCF_000385335.1:WP_020173599.1  17 GRFDGIRRPYGPEEVKRLRGSFPIAYTLAERSANKLWKLMQE----RPYVHSLGAVTGNQAMQMARAgLEAIY 85 
                                           59************************************9864....4689*********************** PP

                             TIGR01346  84 lsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivad 156
                                           lsGWqv++dan+++ ++Pd+++yPa++ P+  ++++k++++ d++++ +++ +           d+++Pi+ad
  NCBI__GCF_000385335.1:WP_020173599.1  86 LSGWQVAADANVAGAMYPDQSLYPANSGPELARKINKTFKRVDEIEHAEGNVT----------RDWFLPIIAD 148
                                           *********************************************98877532..........27******** PP

                             TIGR01346 157 adaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllv 229
                                           a+aGfGG l+vf+++k++ie+G a+vh+edql+sekkCGhl+Gkvl+p+ +h + l aarlaadvmgv+tl+v
  NCBI__GCF_000385335.1:WP_020173599.1 149 AEAGFGGPLNVFEIMKAYIEAGVAAVHFEDQLASEKKCGHLGGKVLLPTAQHERSLSAARLAADVMGVPTLVV 221
                                           ************************************************************************* PP

                             TIGR01346 230 artdaeaatlitsdvdardhefiv 253
                                           artdae+a+litsdvd+rd++fi+
  NCBI__GCF_000385335.1:WP_020173599.1 222 ARTDAESAKLITSDVDERDRPFII 245
                                           ***********************8 PP

  == domain 2  score: 235.4 bits;  conditional E-value: 5.2e-74
                             TIGR01346 353 ertreGfyrvkgg..veaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdk 423
                                            rt eGfyr+k g  +  +i+r+ a+a  +d++W ets Pdl ea+efae+v++kfP+kllayn+sPsfnW +
  NCBI__GCF_000385335.1:WP_020173599.1 248 SRTPEGFYRLKDGtgLAHCISRGLAYAEVSDMLWWETSHPDLGEAREFAEAVHKKFPGKLLAYNCSPSFNWRA 320
                                           59*********8622689******************************************************* PP

                             TIGR01346 424 aleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdvlkhq 493
                                           +l++ +i+kf++elg++Gyk+qf+tlaG+hs +l++++la ++  +Gm ay e +qq e+    +G+ + +hq
  NCBI__GCF_000385335.1:WP_020173599.1 321 KLDKATIEKFQRELGAMGYKYQFVTLAGFHSLNLSMYELALGYKDRGMDAYSE-LQQAEFdleAKGYSATRHQ 392
                                           ****************************************************9.******99889******** PP

                             TIGR01346 494 kesGaeyfdqllklvqgGvsataalaksveedqf 527
                                           +e+G++yfd +   + gG s+t+a+++s+e  qf
  NCBI__GCF_000385335.1:WP_020173599.1 393 REVGTGYFDAVSVAISGGASSTTAMGESTESAQF 426
                                           *********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (438 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: 8.27
//
[ok]

This GapMind analysis is from Jul 25 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 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