GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aceA in Shewanella sp. ANA-3

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 7025792 Shewana3_2942 isocitrate lyase (RefSeq)

Query= reanno::MR1:200655
         (440 letters)



>FitnessBrowser__ANA3:7025792
          Length = 440

 Score =  874 bits (2258), Expect = 0.0
 Identities = 433/440 (98%), Positives = 437/440 (99%)

Query: 1   MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW 60
           MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW
Sbjct: 1   MTKATQTSRQAQIDAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLW 60

Query: 61  DLVNGGSKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA 120
           DLVNGG+KKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA
Sbjct: 61  DLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPA 120

Query: 121 NSVPAVVSRINNSFRRADQIQWSNGVNPEDENFVDYFLPIIADAEAGFGGVLNAFELMKS 180
           NSVPAVV+RINNSFRRADQIQWSNGVNPE+ENFVDYFLPIIADAEAGFGGVLNAFELMKS
Sbjct: 121 NSVPAVVARINNSFRRADQIQWSNGVNPEEENFVDYFLPIIADAEAGFGGVLNAFELMKS 180

Query: 181 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD 240
           MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD
Sbjct: 181 MIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTD 240

Query: 241 ANAADLLTSDCDPYDRDFVTGERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPD 300
           ANAADLLTSDCDPYDRDFVTGERT+EGFYRV AGLDQAISRGLAYAPYADLIWCETAKPD
Sbjct: 241 ANAADLLTSDCDPYDRDFVTGERTSEGFYRVKAGLDQAISRGLAYAPYADLIWCETAKPD 300

Query: 301 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQALSDMGYKYQFITLAG 360
           LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQ LSDMGYKYQFITLAG
Sbjct: 301 LEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMGYKYQFITLAG 360

Query: 361 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV 420
           IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV
Sbjct: 361 IHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTV 420

Query: 421 IQGGHSSVTALTGSTEEEQF 440
           IQGG SSVTALTGSTEEEQF
Sbjct: 421 IQGGQSSVTALTGSTEEEQF 440


Lambda     K      H
   0.317    0.132    0.390 

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: 870
Number of extensions: 25
Number of successful extensions: 1
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: 440
Length of database: 440
Length adjustment: 32
Effective length of query: 408
Effective length of database: 408
Effective search space:   166464
Effective search space used:   166464
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 7025792 Shewana3_2942 (isocitrate lyase (RefSeq))
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.20175.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.2e-209  680.3   6.2   6.2e-118  380.4   0.1    2.0  2  lcl|FitnessBrowser__ANA3:7025792  Shewana3_2942 isocitrate lyase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025792  Shewana3_2942 isocitrate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.4   0.1  6.2e-118  6.2e-118       2     254 ..      14     261 ..      13     262 .. 0.98
   2 !  302.5   2.1   2.4e-94   2.4e-94     353     527 .]     262     440 .]     262     440 .] 1.00

  Alignments for each domain:
  == domain 1  score: 380.4 bits;  conditional E-value: 6.2e-118
                         TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqqaka 78 
                                       + i+k+W  ++rw++++r+y+a++vv lrGs+ +e+++++++a+klw++++   k k+++++lGal+++q++qqaka
  lcl|FitnessBrowser__ANA3:7025792  14 DAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLWDLVNGGAK-KGYVNSLGALTGGQAVQQAKA 89 
                                       5799**********************************************99877.6******************** PP

                         TIGR01346  79 .ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyidylvPiv 154
                                        ++a+ylsGWqv++danl++ ++Pd+++yPa++vP++v r++++++++d++q++++ ++++e      ++dy++Pi+
  lcl|FitnessBrowser__ANA3:7025792  90 gIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAVVARINNSFRRADQIQWSNGVNPEEE-----NFVDYFLPII 161
                                       ********************************************************999887.....69******** PP

                         TIGR01346 155 adadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvar 231
                                       ada+aGfGGvl++f+l+k +i++Gaagvh+edql+s+kkCGh++Gkvlvp+qe+v++lvaarlaadv gvetl++ar
  lcl|FitnessBrowser__ANA3:7025792 162 ADAEAGFGGVLNAFELMKSMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIAR 238
                                       ***************************************************************************** PP

                         TIGR01346 232 tdaeaatlitsdvdardhefivG 254
                                       tda+aa+l+tsd+d++d++f++G
  lcl|FitnessBrowser__ANA3:7025792 239 TDANAADLLTSDCDPYDRDFVTG 261
                                       **********************9 PP

  == domain 2  score: 302.5 bits;  conditional E-value: 2.4e-94
                         TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkaledde 429
                                       ert+eGfyrvk+g+++ai+r+ a+aPyadl+W+et++Pdleea++fae++++++Pd+llayn+sPsfnW+k+l+d +
  lcl|FitnessBrowser__ANA3:7025792 262 ERTSEGFYRVKAGLDQAISRGLAYAPYADLIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDAT 338
                                       7**************************************************************************** PP

                         TIGR01346 430 ikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvlkhqkesGaeyfd 502
                                       i++f++el+d+Gyk+qfitlaG+h +++++fdla+d+a+ eGmk+yvekvq+ e+   ++G+++++hq+e+G++yfd
  lcl|FitnessBrowser__ANA3:7025792 339 IARFQQELSDMGYKYQFITLAGIHNMWYNMFDLAYDYARgEGMKHYVEKVQEVEFaaaKKGYTFVAHQQEVGTGYFD 415
                                       ********************************************************999****************** PP

                         TIGR01346 503 qllklvqgGvsataalaksveedqf 527
                                       q+++++qgG s+++al++s+ee+qf
  lcl|FitnessBrowser__ANA3:7025792 416 QVTTVIQGGQSSVTALTGSTEEEQF 440
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (440 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 2.88
//
[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:

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:

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:

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:

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