Alignments for a candidate for aceA in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Halorhodospira halophila SL1

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_011814191.1 HHAL_RS07095 isocitrate lyase

Query= reanno::PV4:5208774
         (450 letters)



>NCBI__GCF_000015585.1:WP_011814191.1
          Length = 422

 Score =  586 bits (1511), Expect = e-172
 Identities = 298/426 (69%), Positives = 347/426 (81%), Gaps = 10/426 (2%)

Query: 25  AIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENTLATRGAEKLWQLVNGGAKKGYVNS 84
           AI++DWAENPRW GV+R Y A++VV LRG++  E +LA +GAEKLWQ ++   +  YVN+
Sbjct: 7   AIERDWAENPRWKGVQRGYGADEVVRLRGTVHVEYSLARQGAEKLWQSMH---EMPYVNA 63

Query: 85  LGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAVVQRINNSF 144
           LGALTG QA+QQ KAG+ AIYLSGWQVAADANL  TMYPDQSLYPANSVPAVV RINN+ 
Sbjct: 64  LGALTGNQALQQVKAGLNAIYLSGWQVAADANLGQTMYPDQSLYPANSVPAVVDRINNAL 123

Query: 145 RRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGGVLNAYELMKNMIDAGAAGVHFEDQ 204
            RAD+I  +    P      D+  PIVADAEAGFGGVLNA+ELMK MI AGAAGVHFEDQ
Sbjct: 124 LRADEINHAEGNPP-----FDFMKPIVADAEAGFGGVLNAFELMKGMIRAGAAGVHFEDQ 178

Query: 205 LASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSGVPTLVIARTDANAADLLTSDCDPY 264
           LASVKKCGHMGGKVL+PTQEAVQKL++ARLAAD   VPT+++ARTDA AADLLTSD D  
Sbjct: 179 LASVKKCGHMGGKVLLPTQEAVQKLIAARLAADTMDVPTILVARTDAEAADLLTSDVDDN 238

Query: 265 DRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYADLIWCETAKPDLEEARRFAEAIHAQ 324
           D+ FITGERT+EGF+R   GI+QAISRGLAYAPYAD+IWCET KPDLE AR FA+AIH +
Sbjct: 239 DKPFITGERTAEGFFRTKPGIEQAISRGLAYAPYADVIWCETGKPDLEFAREFAQAIHEK 298

Query: 325 YPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMGYKYQFITLAGIHNMWYNMFDLAYD 384
           YP +LLAYNCSPSFNW  NLD+ATI +FQ EL  MG+K+QFITLAG H++ Y+MF+LA  
Sbjct: 299 YPGKLLAYNCSPSFNWAGNLDEATIRKFQDELGKMGFKFQFITLAGFHSLNYSMFELARG 358

Query: 385 YARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDKVTNVIQGGESSVTALTGS 444
           Y   + M+ Y E +Q+ EFAA K GYT   HQ+EVG GYFD+VTNVIQGG+SSVTAL GS
Sbjct: 359 YKERQ-MEAYSE-LQQAEFAAEKHGYTATRHQREVGAGYFDQVTNVIQGGQSSVTALKGS 416

Query: 445 TEEEQF 450
           TEEEQF
Sbjct: 417 TEEEQF 422


Lambda     K      H
   0.316    0.132    0.389 

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: 629
Number of extensions: 17
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: 450
Length of database: 422
Length adjustment: 32
Effective length of query: 418
Effective length of database: 390
Effective search space:   163020
Effective search space used:   163020
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_011814191.1 HHAL_RS07095 (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.704271.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-188  611.7   3.0   6.6e-106  340.7   0.1    2.0  2  NCBI__GCF_000015585.1:WP_011814191.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_011814191.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.7   0.1  6.6e-106  6.6e-106       3     254 ..       7     245 ..       5     246 .. 0.97
   2 !  271.8   0.8   5.1e-85   5.1e-85     353     527 .]     246     422 .]     246     422 .] 0.99

  Alignments for each domain:
  == domain 1  score: 340.7 bits;  conditional E-value: 6.6e-106
                             TIGR01346   3 eiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvqvsqq 75 
                                            i+++W  ++rw++++r y a++vv+lrG+v+ e  l++++a+klw+ +++      ++++lGal+++q++qq
  NCBI__GCF_000015585.1:WP_011814191.1   7 AIERDWAENPRWKGVQRGYGADEVVRLRGTVHVEYSLARQGAEKLWQSMHE----MPYVNALGALTGNQALQQ 75 
                                           589*******************************************99864....468*************** PP

                             TIGR01346  76 aka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeeelkelyi 147
                                           +ka l+a+ylsGWqv++danl + ++Pd+++yPa++vP++v+r+++all++d++++ +++          ++ 
  NCBI__GCF_000015585.1:WP_011814191.1  76 VKAgLNAIYLSGWQVAADANLGQTMYPDQSLYPANSVPAVVDRINNALLRADEINHAEGN----------PPF 138
                                           *****************************************************9987653..........589 PP

                             TIGR01346 148 dylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrlvaarlaad 220
                                           d+++Pivada+aGfGGvl++f+l+k +i +Gaagvh+edql+s+kkCGh++Gkvl+p+qe+v++l+aarlaad
  NCBI__GCF_000015585.1:WP_011814191.1 139 DFMKPIVADAEAGFGGVLNAFELMKGMIRAGAAGVHFEDQLASVKKCGHMGGKVLLPTQEAVQKLIAARLAAD 211
                                           ************************************************************************* PP

                             TIGR01346 221 vmgvetllvartdaeaatlitsdvdardhefivG 254
                                            m+v+t+lvartdaeaa+l+tsdvd+ d++fi+G
  NCBI__GCF_000015585.1:WP_011814191.1 212 TMDVPTILVARTDAEAADLLTSDVDDNDKPFITG 245
                                           *********************************9 PP

  == domain 2  score: 271.8 bits;  conditional E-value: 5.1e-85
                             TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdkal 425
                                           ert+eGf+r+k g+e+ai+r+ a+aPyad++W+et++Pdle a+efa+++++k+P+kllayn+sPsfnW  +l
  NCBI__GCF_000015585.1:WP_011814191.1 246 ERTAEGFFRTKPGIEQAISRGLAYAPYADVIWCETGKPDLEFAREFAQAIHEKYPGKLLAYNCSPSFNWAGNL 318
                                           7************************************************************************ PP

                             TIGR01346 426 eddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGvdvlkhqke 495
                                           ++ +i+kf++elg++G+kfqfitlaG+hs ++++f+la+++ ++ m+ay e +qq e+   ++G+++ +hq+e
  NCBI__GCF_000015585.1:WP_011814191.1 319 DEATIRKFQDELGKMGFKFQFITLAGFHSLNYSMFELARGYKERQMEAYSE-LQQAEFaaeKHGYTATRHQRE 390
                                           **************************************************9.*******999*********** PP

                             TIGR01346 496 sGaeyfdqllklvqgGvsataalaksveedqf 527
                                           +Ga+yfdq+++++qgG s+++al++s+ee+qf
  NCBI__GCF_000015585.1:WP_011814191.1 391 VGAGYFDQVTNVIQGGQSSVTALKGSTEEEQF 422
                                           *******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (422 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.29
//
[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