Alignments for a candidate for cimA in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Mesorhizobium ciceri WSM1271

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate YP_004143951.1 Mesci_4792 2-isopropylmalate synthase

Query= BRENDA::Q74C76
         (528 letters)



>NCBI__GCF_000185905.1:YP_004143951.1
          Length = 538

 Score =  456 bits (1173), Expect = e-132
 Identities = 259/531 (48%), Positives = 338/531 (63%), Gaps = 16/531 (3%)

Query: 6   LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKEKL 65
           L+DTTLRDG Q   I F VEDKI IA  LD  G+ Y+EGG+PG+NP D AFF++ + E+ 
Sbjct: 8   LFDTTLRDGQQTPGIDFSVEDKIAIAKLLDAFGLDYVEGGYPGANPTDTAFFQEKRTER- 66

Query: 66  SQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLEL 125
             AK  AFG T+RA V+   D  L +L+Q++ D      K+WD+HV  AL  + EENL+ 
Sbjct: 67  --AKFVAFGMTKRAGVSASNDPGLASLVQSKSDAICFVAKSWDYHVRVALGCTNEENLDA 124

Query: 126 IFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMPF 185
           I  S+E   A   E   D EHFFDG+KANPDYA+   + A DA A  +VLCDTNGGT P 
Sbjct: 125 IKASVEAAIAAGKEALVDCEHFFDGFKANPDYALACARTAYDAGARWVVLCDTNGGTQPS 184

Query: 186 ELVEIIREV-RKHITAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNAN 243
           E+  I+ +V    I+   LGIH H+D+  AVANSL AV  G+ Q+QGT+NG GERCGNAN
Sbjct: 185 EVRAIVEKVILSGISGDHLGIHAHDDTGQAVANSLAAVEAGVRQIQGTLNGIGERCGNAN 244

Query: 244 LCSIIPALKLKMK-----RECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHK 298
           L SI+P L LK          I  + L  +  LSR   EL N +P     YVG SAFA K
Sbjct: 245 LISIVPTLALKPAFADRFETGISAEALTGISRLSRAFDELLNRAPEAQAPYVGASAFATK 304

Query: 299 GGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLE 358
            G+H SA+ + P TYEH+ PE VGN  RV+VSD  G++N LA+     I++   D     
Sbjct: 305 AGIHASALAKEPATYEHVPPETVGNRRRVMVSDQGGKANFLAELRRRGIEVPKDDHRLDA 364

Query: 359 ILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHE---DQKPLS 415
           ++  +KE E  GY +EGA+ASFELL ++ L    +FF+V  FR + E+R +     K +S
Sbjct: 365 LISVVKEREAEGYAYEGADASFELLARKMLHGLPEFFNVTSFRCMVERRFDANGQLKTVS 424

Query: 416 EATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGT 475
           EA + V V G+ + + AEG+GPVNALD ALRK L KF   + +++L D+KVR+L    GT
Sbjct: 425 EAIVKVVVDGEEKMSVAEGHGPVNALDIALRKDLGKFQGEIADMELADFKVRIL--NGGT 482

Query: 476 ASSIRVLIESGD-KESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIEG 525
            +  RVLIES D   +RW TVGVSENI+DAS+QAL+DS+ YKL K+ E+ G
Sbjct: 483 EAITRVLIESHDGTGARWWTVGVSENIIDASFQALMDSIVYKLMKNREMAG 533


Lambda     K      H
   0.317    0.135    0.387 

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: 679
Number of extensions: 30
Number of successful extensions: 7
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: 528
Length of database: 538
Length adjustment: 35
Effective length of query: 493
Effective length of database: 503
Effective search space:   247979
Effective search space used:   247979
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: 52 (24.6 bits)

Align candidate YP_004143951.1 Mesci_4792 (2-isopropylmalate synthase)
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.6362.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-183  595.5   0.0   4.5e-183  595.2   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004143951.1  Mesci_4792 2-isopropylmalate syn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004143951.1  Mesci_4792 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.2   0.0  4.5e-183  4.5e-183       2     522 ..       6     530 ..       5     533 .. 0.96

  Alignments for each domain:
  == domain 1  score: 595.2 bits;  conditional E-value: 4.5e-183
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               l+l+dttlrdG q+ G+ +s+edki ia+ ld +G++y+eGG+pganp d+aff++      ++ak va
  lcl|NCBI__GCF_000185905.1:YP_004143951.1   6 LYLFDTTLRDGQQTPGIDFSVEDKIAIAKLLDAFGLDYVEGGYPGANPTDTAFFQEK---RTERAKFVA 71 
                                               89****************************************************865...56799**** PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+ t+r  +  ++d+ l +l+++++  +    kswd hv  al  t eenl+ i  +ve     ++e +
  lcl|NCBI__GCF_000185905.1:YP_004143951.1  72 FGMTKRAGVSASNDPGLASLVQSKSDAICFVAKSWDYHVRVALGCTNEENLDAIKASVEAAIAAGKEAL 140
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkr.lkdpqlGihahn 207
                                                d ehffdG+kanp+yal+  ++a +aGa w+vl+dtnGGt p e+  i++kv  + +   +lGihah+
  lcl|NCBI__GCF_000185905.1:YP_004143951.1 141 VDCEHFFDGFKANPDYALACARTAYDAGARWVVLCDTNGGTQPSEVRAIVEKVILSgISGDHLGIHAHD 209
                                               ****************************************************9755278999******* PP

                                 TIGR00977 208 dsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgl....d.viekenlkklteva 271
                                               d++ avansl+aveaG +q+qGt+nG+GercGnanl s++p l lk  +    +  i  e l  +  ++
  lcl|NCBI__GCF_000185905.1:YP_004143951.1 210 DTGQAVANSLAAVEAGVRQIQGTLNGIGERCGNANLISIVPTLALKPAFadrfEtGISAEALTGISRLS 278
                                               **********************************************8873323335999********** PP

                                 TIGR00977 272 rlvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvlek 340
                                               r   e+ n+a++ ++pyvG safa k G+h+sa+ ++p tyeh+ pe vGn+r+++vs++ Gk+n l  
  lcl|NCBI__GCF_000185905.1:YP_004143951.1 279 RAFDELLNRAPEAQAPYVGASAFATKAGIHASALAKEPATYEHVPPETVGNRRRVMVSDQGGKANFLAE 347
                                               ********************************************************************* PP

                                 TIGR00977 341 lkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrde 409
                                               l+  Gie+ +++ ++  +++ +ke e++Gy +e+a+as+ell r++l    ++f+v++fr ++++r d+
  lcl|NCBI__GCF_000185905.1:YP_004143951.1 348 LRRRGIEVPKDDHRLDALISVVKEREAEGYAYEGADASFELLARKMLHGLPEFFNVTSFRCMVERRFDA 416
                                               ********************************************************************9 PP

                                 TIGR00977 410 e.slse.aeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGts 476
                                               +  l++ +ea v+v v+g e++ +aeG+Gpv+ald alrk l kf  +++d++l d+kvriln+  Gt+
  lcl|NCBI__GCF_000185905.1:YP_004143951.1 417 NgQLKTvSEAIVKVVVDGEEKMSVAEGHGPVNALDIALRKDLGKFQGEIADMELADFKVRILNG--GTE 483
                                               9655543899****************************************************97..9** PP

                                 TIGR00977 477 aktrvliessdGk.rrwgtvGvseniieasytallesieyklrkdee 522
                                               a trvlies dG   rw tvGvsenii+as++al++si+ykl+k+ e
  lcl|NCBI__GCF_000185905.1:YP_004143951.1 484 AITRVLIESHDGTgARWWTVGVSENIIDASFQALMDSIVYKLMKNRE 530
                                               ************7479***************************9876 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: 00:00:00.03
# Mc/sec: 7.65
//
[ok]

This GapMind analysis is from Apr 10 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