Alignments for a candidate for cimA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Sinorhizobium meliloti 1021

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate SMc02546 SMc02546 alpha-isopropylmalate/homocitrate synthase family transferase

Query= BRENDA::Q74C76
         (528 letters)



>FitnessBrowser__Smeli:SMc02546
          Length = 538

 Score =  452 bits (1164), Expect = e-131
 Identities = 257/534 (48%), Positives = 337/534 (63%), Gaps = 16/534 (2%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           + L+DTTLRDG Q   I F VEDKI IA  LD+ G+ Y+EGG+PG+NP D  FFK  + +
Sbjct: 6   IYLFDTTLRDGQQTPGIDFSVEDKIAIASLLDQFGMDYVEGGYPGANPTDTEFFKCRRTD 65

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
           K   A   AFG T+RA V+   D  L  L+ A+ D   +  K+WD+HV  AL  + EENL
Sbjct: 66  K---ASFVAFGMTKRAGVSASNDPGLSALLSAKSDAICLVAKSWDYHVEVALGCTNEENL 122

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
           + I  S+E + A+  E   D EHFFDGYKAN  YA+   K A +A A  +VLCDTNGGT 
Sbjct: 123 DNIRASVEAVVASGREAMVDCEHFFDGYKANSAYALACAKTAFEAGARWVVLCDTNGGTQ 182

Query: 184 PFELVEIIREVRKHIT--APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGN 241
           P E+ EI+  V       A LGIH HND+  AVANSL AV  G+ Q+QGT+NG GERCGN
Sbjct: 183 PPEIREIVSAVIAEGVPGANLGIHAHNDTGQAVANSLAAVEAGVRQIQGTLNGIGERCGN 242

Query: 242 ANLCSIIPALKLKMKREC-----IGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFA 296
           ANL ++I  L LK          I  ++L++L  L+    EL N SP+    YVG SAFA
Sbjct: 243 ANLVTLIATLALKETYSSRFETGIDAERLQELTKLAHAFDELLNRSPDPQAPYVGASAFA 302

Query: 297 HKGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVT 356
            K G+H SA+ + P TYEH+ PE VGN+ +V+VSD  G++N +   +   I +   DP  
Sbjct: 303 TKAGIHASALLKDPRTYEHVAPESVGNLRKVMVSDQGGKANFINALKRRGITVSKDDPRL 362

Query: 357 LEILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQ---KP 413
            +++  +KE E  GY +EGA+ASF LL  R LGT   FF V  FRV+ E+R +     K 
Sbjct: 363 DKLISIVKEREATGYAYEGADASFALLASRILGTVPDFFRVESFRVMVERRFDANGKLKT 422

Query: 414 LSEATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQ 473
           +SEA + V V G+   + AEG+GPVNALD ALRK L K+   + +++L DYKVR+L    
Sbjct: 423 VSEAVVRVIVDGETMMSVAEGHGPVNALDLALRKDLGKYQSEIADLELADYKVRIL--NG 480

Query: 474 GTASSIRVLIESGDKE-SRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIEGS 526
           GT +  RVLIES D+  +RW TVGVS+NI+DAS+QAL+DS+ YKL K+ +  GS
Sbjct: 481 GTEAVTRVLIESTDRSGARWWTVGVSDNIIDASFQALMDSIVYKLLKNRDQVGS 534


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: 692
Number of extensions: 33
Number of successful extensions: 6
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 SMc02546 SMc02546 (alpha-isopropylmalate/homocitrate synthase family transferase)
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.23131.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.5e-188  610.6   0.1   1.1e-187  610.4   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc02546  SMc02546 alpha-isopropylmalate/h


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02546  SMc02546 alpha-isopropylmalate/homocitrate synthase family transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.4   0.1  1.1e-187  1.1e-187       2     522 ..       6     530 ..       5     534 .. 0.96

  Alignments for each domain:
  == domain 1  score: 610.4 bits;  conditional E-value: 1.1e-187
                           TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrr 76 
                                         ++l+dttlrdG q+ G+ +s+edki ia  ld++G++y+eGG+pganp d++ff+  +    ++a  vaf+ t+r
  lcl|FitnessBrowser__Smeli:SMc02546   6 IYLFDTTLRDGQQTPGIDFSVEDKIAIASLLDQFGMDYVEGGYPGANPTDTEFFKCRR---TDKASFVAFGMTKR 77 
                                         89****************************************************7655...5789********** PP

                           TIGR00977  77 pdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGyka 151
                                           +  ++d+ l al++a++  + +  kswd hve al  t eenl+ i  +ve +   ++e + d ehffdGyka
  lcl|FitnessBrowser__Smeli:SMc02546  78 AGVSASNDPGLSALLSAKSDAICLVAKSWDYHVEVALGCTNEENLDNIRASVEAVVASGREAMVDCEHFFDGYKA 152
                                         *************************************************************************** PP

                           TIGR00977 152 npeyalktlkvaekaGadwlvladtnGGtlpheieeitkkv.kkrlkdpqlGihahndsetavansllaveaGav 225
                                         n  yal+  k+a +aGa w+vl+dtnGGt p ei ei+  v  + +  ++lGihahnd++ avansl+aveaG +
  lcl|FitnessBrowser__Smeli:SMc02546 153 NSAYALACAKTAFEAGARWVVLCDTNGGTQPPEIREIVSAViAEGVPGANLGIHAHNDTGQAVANSLAAVEAGVR 227
                                         **************************************99735779***************************** PP

                           TIGR00977 226 qvqGtinGlGercGnanlcslipnlqlklgldv.....iekenlkkltevarlvaeivnlaldenmpyvGesafa 295
                                         q+qGt+nG+GercGnanl +li  l lk  +       i+ e+l++lt++a+   e+ n+++d ++pyvG safa
  lcl|FitnessBrowser__Smeli:SMc02546 228 QIQGTLNGIGERCGNANLVTLIATLALKETYSSrfetgIDAERLQELTKLAHAFDELLNRSPDPQAPYVGASAFA 302
                                         ****************************99864334459************************************ PP

                           TIGR00977 296 hkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGy 370
                                          k G+h+sa+ ++p+tyeh++pe vGn rk++vs++ Gk+n ++ lk  Gi + +++p++ k+++ +ke e+ Gy
  lcl|FitnessBrowser__Smeli:SMc02546 303 TKAGIHASALLKDPRTYEHVAPESVGNLRKVMVSDQGGKANFINALKRRGITVSKDDPRLDKLISIVKEREATGY 377
                                         *************************************************************************** PP

                           TIGR00977 371 hfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee.slse.aeatvrvsvegaeeltaaeGnGpvsaldr 443
                                          +e+a+as+ ll  + lG++ ++f v++frv++++r d++  l++ +ea vrv v+g  ++ +aeG+Gpv+ald 
  lcl|FitnessBrowser__Smeli:SMc02546 378 AYEGADASFALLASRILGTVPDFFRVESFRVMVERRFDANgKLKTvSEAVVRVIVDGETMMSVAEGHGPVNALDL 452
                                         **************************************99655543899************************** PP

                           TIGR00977 444 alrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvseniieasytallesieykl 517
                                         alrk l k+  +++dl+l dykvriln+  Gt+a trvlies+d    rw tvGvs+nii+as++al++si+ykl
  lcl|FitnessBrowser__Smeli:SMc02546 453 ALRKDLGKYQSEIADLELADYKVRILNG--GTEAVTRVLIESTDRSgARWWTVGVSDNIIDASFQALMDSIVYKL 525
                                         **************************97..9************96427999************************ PP

                           TIGR00977 518 rkdee 522
                                          k+  
  lcl|FitnessBrowser__Smeli:SMc02546 526 LKNRD 530
                                         99765 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.19
//
[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