Alignments for a candidate for cimA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Desulfovibrio vulgaris Hildenborough

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate 207383 DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein

Query= reanno::DvH:207383
         (538 letters)



>MicrobesOnline__882:207383
          Length = 538

 Score = 1061 bits (2745), Expect = 0.0
 Identities = 538/538 (100%), Positives = 538/538 (100%)

Query: 1   MRRQIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKE 60
           MRRQIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKE
Sbjct: 1   MRRQIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKE 60

Query: 61  IRNYNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDG 120
           IRNYNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDG
Sbjct: 61  IRNYNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDG 120

Query: 121 RRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTN 180
           RRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTN
Sbjct: 121 RRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTN 180

Query: 181 GGTLPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGER 240
           GGTLPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGER
Sbjct: 181 GGTLPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGER 240

Query: 241 CGNANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFA 300
           CGNANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFA
Sbjct: 241 CGNANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFA 300

Query: 301 HKGGVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVV 360
           HKGGVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVV
Sbjct: 301 HKGGVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVV 360

Query: 361 KGLMNELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQENDLEPM 420
           KGLMNELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQENDLEPM
Sbjct: 361 KGLMNELKKKASLGYDYAAAEASVELLLLRKLARRGVREFFKLIQFRVLESKQENDLEPM 420

Query: 421 SEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTGTET 480
           SEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTGTET
Sbjct: 421 SEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTGTET 480

Query: 481 DGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEHVQRGMTD 538
           DGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEHVQRGMTD
Sbjct: 481 DGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEHVQRGMTD 538


Lambda     K      H
   0.318    0.134    0.382 

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: 1008
Number of extensions: 32
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: 538
Length of database: 538
Length adjustment: 35
Effective length of query: 503
Effective length of database: 503
Effective search space:   253009
Effective search space used:   253009
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: 52 (24.6 bits)

Align candidate 207383 DVU1914 (2-isopropylmalate synthase/homocitrate synthase family protein)
to HMM TIGR00977 (cimA: citramalate synthase (EC 2.3.1.182))

# 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/TIGR00977.hmm
# target sequence database:        /tmp/gapView.22252.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00977  [M=526]
Accession:   TIGR00977
Description: citramal_synth: citramalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.7e-212  689.8   0.1   1.1e-211  689.5   0.1    1.0  1  lcl|MicrobesOnline__882:207383  DVU1914 2-isopropylmalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207383  DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.5   0.1  1.1e-211  1.1e-211       2     522 ..       5     531 ..       4     535 .. 0.97

  Alignments for each domain:
  == domain 1  score: 689.5 bits;  conditional E-value: 1.1e-211
                       TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrrpdkk 80 
                                     ++lydttlrdG+q e + l   dk++ia +ld+lGi yieGGwpg+np dvaff+++++ nlk+ak++af+st  p + 
  lcl|MicrobesOnline__882:207383   5 IHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKEIRNYNLKQAKISAFGSTHHPSHT 83 
                                     89***************************************************************************** PP

                       TIGR00977  81 veedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGykanpeyalkt 159
                                      e+d++l+a+  a t   +ifGks + h  eal+     nl++i+d++++lk+++ ev +daehffdGy+ n  yal++
  lcl|MicrobesOnline__882:207383  84 AENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDGRRNLDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEV 162
                                     ******************************************************************************* PP

                       TIGR00977 160 lkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllaveaGavqvqGtinGlGerc 238
                                     l+ a++aG d+lvl+dtnGGtlphe+++i++ v+++l +++lGihahnd e+avans++av+aGavqvqGt+nG+Gerc
  lcl|MicrobesOnline__882:207383 163 LRRAHEAGGDVLVLCDTNGGTLPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGERC 241
                                     ******************************************************************************* PP

                       TIGR00977 239 Gnanlcslipnlqlkl..gldviekenlkkltevarlvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehi 315
                                     Gnanl s+ip l lk    + ++++ +l++lt v+ +v+e++nl++ ++ p+vG+safahkGGvhvsav+rn++ yehi
  lcl|MicrobesOnline__882:207383 242 GNANLSSVIPILELKSagAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFAHKGGVHVSAVNRNATLYEHI 320
                                     ***************74359*********************************************************** PP

                       TIGR00977 316 dpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkr..kk 392
                                      pe vGn++++ ++elaG+sn+++ ++ +G+++d+++p v+ +++++k+    Gy++ aaeas+ell+ ++l +r  ++
  lcl|MicrobesOnline__882:207383 321 TPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVVKGLMNELKKKASLGYDYAAAEASVELLLLRKLARRgvRE 399
                                     ********************************************************************99998754489 PP

                       TIGR00977 393 yfevdgfrvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilne 471
                                     +f++  frvl  k+ ++   + +ea v v veg  e+taa G Gpv+ald+alrkal  fyp++++++l+d+kvr+l +
  lcl|MicrobesOnline__882:207383 400 FFKLIQFRVLESKQEND-LEPMSEASVMVEVEGIIEHTAATGRGPVNALDNALRKALSSFYPRIREMRLLDFKVRVLTG 477
                                     **********9998887.6788999999************************************************975 PP

                       TIGR00977 472 ...saGtsaktrvliessdGkrrwgtvGvseniieasytallesieyklrkdee 522
                                        + Gt +++rvlies d + rw tvGvs niieas++al +s+ ykl kde 
  lcl|MicrobesOnline__882:207383 478 tetDGGTASTVRVLIESGDADSRWVTVGVSYNIIEASWQALADSMTYKLYKDEH 531
                                     222679*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (538 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: 9.75
//
[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:

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