Alignments for a candidate for aceA in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Sinorhizobium medicae WSM419

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_011974516.1 SMED_RS01540 isocitrate lyase

Query= BRENDA::Q8RPZ0
         (436 letters)



>NCBI__GCF_000017145.1:WP_011974516.1
          Length = 429

 Score =  561 bits (1446), Expect = e-164
 Identities = 281/414 (67%), Positives = 328/414 (79%), Gaps = 4/414 (0%)

Query: 26  ATEPRWRDIERTYGAEEVIRLSGSVREEHTLARRGADRLWRQLHELDYVHALGALTGGQA 85
           A E R+  IER Y AE+V RL GSV   ++LA  GA+RLW+ +HE D+V+ALGAL+G QA
Sbjct: 11  APEGRFDGIERPYSAEDVKRLRGSVEIRYSLAEMGANRLWKLIHEEDFVNALGALSGNQA 70

Query: 86  VQQVRAGLQAIYLFGWQVAADANQAGHTYPDQSLYPANSVPQVVRRINNALLRADQIATA 145
           +Q VRAGL+AIYL GWQVAADAN A   YPDQSLYPAN+ P++ +RIN  L RADQI TA
Sbjct: 71  MQMVRAGLKAIYLSGWQVAADANTASAMYPDQSLYPANAAPELAKRINRTLQRADQIETA 130

Query: 146 ENAGDGTD-WLAPIVADAEAGFGGPLNAFELTKAMIEAGAAGIHYEDQLASEKKCGHLGG 204
           E  G   D W APIVADAEAGFGGPLNAFE+ KA IEAGAAG+HYEDQLASEKKCGHLGG
Sbjct: 131 EGKGLSVDTWFAPIVADAEAGFGGPLNAFEIMKAFIEAGAAGVHYEDQLASEKKCGHLGG 190

Query: 205 KVLVPTAQHIRTLNAARLAADIADVPTVIIARTDALAASLITSDVDERDAEF--LTGERT 262
           KVL+PTA HIR LNAARLAAD+   PT++IARTDA AA L+TSD+DERD  F  +   RT
Sbjct: 191 KVLIPTAAHIRNLNAARLAADVMGTPTLVIARTDAEAAKLLTSDIDERDRPFVDIDAGRT 250

Query: 263 AEGFHRVRNGMAPVIARGLAYAPYADLLWMETGTPDLAQAREFAEAIHAQYPEQLLAYNC 322
            EGF++VRNG+ P IAR +AYAP+ DL+W ET  PDL QAR+FAE +H  YP +LLAYNC
Sbjct: 251 VEGFYQVRNGIEPCIARAIAYAPHCDLIWCETSKPDLEQARKFAEGVHKAYPGKLLAYNC 310

Query: 323 SPSFNWRAALDDDRIAKFQRELGAMGYRFQFITLAGFHSLNHAMFDLARGYAEHGMTAYV 382
           SPSFNW+  LDD  IAKFQRELGAMGY+FQFITLAGFH LN+ MF+LARGY +  M AY 
Sbjct: 311 SPSFNWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYKDRQMAAYS 370

Query: 383 DLQEREFAAQADGFTAVRHQREVGTGYFDLVSTAVNPA-SSTTALSGSTEEEQF 435
           +LQE EFAA+A+G+TA +HQREVGTGYFD VS A+    SSTTA+  STE +QF
Sbjct: 371 ELQEAEFAAEANGYTATKHQREVGTGYFDAVSVAITGGQSSTTAMKESTEHDQF 424


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: 567
Number of extensions: 25
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: 429
Length adjustment: 32
Effective length of query: 404
Effective length of database: 397
Effective search space:   160388
Effective search space used:   160388
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_011974516.1 SMED_RS01540 (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.2029469.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-179  581.5   1.6      1e-97  313.6   0.0    2.0  2  NCBI__GCF_000017145.1:WP_011974516.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017145.1:WP_011974516.1  
   #    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     245 .. 0.97
   2 !  269.7   0.4   2.1e-84   2.1e-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+ysa+dv +lrGsv+ +  l++++a++lw+++++e+     +++lGal ++q++q+++a l+a+y
  NCBI__GCF_000017145.1:WP_011974516.1  14 GRFDGIERPYSAEDVKRLRGSVEIRYSLAEMGANRLWKLIHEED----FVNALGALSGNQAMQMVRAgLKAIY 82 
                                           69*********************9999*************9775....59*********************** PP

                             TIGR01346  84 lsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPivad 156
                                           lsGWqv++dan+++ ++Pd+++yPa++ P+  +r++++l+++d++++ +++  + +         ++ Pivad
  NCBI__GCF_000017145.1:WP_011974516.1  83 LSGWQVAADANTASAMYPDQSLYPANAAPELAKRINRTLQRADQIETAEGKGLSVD--------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_000017145.1:WP_011974516.1 148 AEAGFGGPLNAFEIMKAFIEAGAAGVHYEDQLASEKKCGHLGGKVLIPTAAHIRNLNAARLAADVMGTPTLVI 220
                                           ************************************************************************* PP

                             TIGR01346 230 artdaeaatlitsdvdardhefi 252
                                           artdaeaa+l+tsd+d+rd++f+
  NCBI__GCF_000017145.1:WP_011974516.1 221 ARTDAEAAKLLTSDIDERDRPFV 243
                                           *********************97 PP

  == domain 2  score: 269.7 bits;  conditional E-value: 2.1e-84
                             TIGR01346 347 ffdwelertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsf 419
                                           f d +  rt eGfy+v++g+e++i+ra a+aP+ dl+W+ets+Pdle+a++faegv++ +P+kllayn+sPsf
  NCBI__GCF_000017145.1:WP_011974516.1 242 FVDIDAGRTVEGFYQVRNGIEPCIARAIAYAPHCDLIWCETSKPDLEQARKFAEGVHKAYPGKLLAYNCSPSF 314
                                           8899********************************************************************* PP

                             TIGR01346 420 nWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdv 489
                                           nW+k+l+d +i+kf++elg++GykfqfitlaG+h  ++++f+la+++  + m ay e +q+ e+    +G+++
  NCBI__GCF_000017145.1:WP_011974516.1 315 NWKKNLDDATIAKFQRELGAMGYKFQFITLAGFHQLNYGMFELARGYKDRQMAAYSE-LQEAEFaaeANGYTA 386
                                           ********************************************************9.******9999***** PP

                             TIGR01346 490 lkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                            khq+e+G++yfd +   + gG s+t+a+++s+e dqf
  NCBI__GCF_000017145.1:WP_011974516.1 387 TKHQREVGTGYFDAVSVAITGGQSSTTAMKESTEHDQF 424
                                           *************************************9 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 5.91
//
[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