Alignments for a candidate for cimA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for cimA in Synechococcus elongatus PCC 7942

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate Synpcc7942_0428 Synpcc7942_0428 putative alpha-isopropylmalate/homocitrate synthase family transferase

Query= BRENDA::Q74C76
         (528 letters)



>FitnessBrowser__SynE:Synpcc7942_0428
          Length = 542

 Score =  551 bits (1419), Expect = e-161
 Identities = 278/522 (53%), Positives = 366/522 (70%), Gaps = 10/522 (1%)

Query: 4   VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63
           + +YDTTLRDG Q E +S  +EDK+RIAH LD +G+ +IEGGWPG+NPKDV FF ++++ 
Sbjct: 9   IAVYDTTLRDGAQREGLSLSLEDKLRIAHCLDRLGVKFIEGGWPGANPKDVQFFWELQQR 68

Query: 64  KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123
            L QA++ AF STRR      +D  LK L+ A     TIFGK+WD HV E L+ SL+ENL
Sbjct: 69  PLQQAEVVAFCSTRRPGQIAGEDELLKALLAAGTTWVTIFGKSWDLHVVEGLKTSLDENL 128

Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183
            +I DS+ YL+     V YDAEH+FDGY ANPDYA++TL AA +A A+ IVLCDTNGG +
Sbjct: 129 VMISDSIAYLRTCDRRVIYDAEHWFDGYLANPDYALQTLAAAIEAGAEWIVLCDTNGGCL 188

Query: 184 PFELVEIIREVRKHI-------TAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGF 235
           P ++ EI+  V           T P LGIHTHNDSE AVAN++ AV  G   V GTING+
Sbjct: 189 PHQISEIVAAVLDRFPSLAPDQTGPQLGIHTHNDSETAVANAIAAVQAGARMVHGTINGY 248

Query: 236 GERCGNANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAF 295
           GERCGNANLCS+IP L+LK+  +C+  +QL +L   SR V E+ NL+P+ H AYVG SAF
Sbjct: 249 GERCGNANLCSVIPNLQLKLGYDCVETEQLMQLTATSRLVSEIVNLAPDDHAAYVGQSAF 308

Query: 296 AHKGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPV 355
           AHKGG+HVSA++R+P TYEH+RPE VGN+ R+++S+ SG SN+LAKA  F + +   DP 
Sbjct: 309 AHKGGIHVSAVERNPLTYEHIRPEQVGNLRRIVISEQSGLSNVLAKARSFGLDLQRNDPA 368

Query: 356 TLEILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLS 415
             ++L  +KE+E++GYQFE AEASF+LLM+ A G    FF +  F V   K+ ++   L 
Sbjct: 369 CRDLLARLKELESQGYQFEAAEASFDLLMREATGDRPHFFDLKDFHVHCSKQRQELNAL- 427

Query: 416 EATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGT 475
            AT+ V V G+    +AEGNGPV+ALD ALRKA+  FYP + +  L DYKVR+L    GT
Sbjct: 428 -ATVKVAVTGRDILESAEGNGPVSALDAALRKAIGSFYPAVMQFHLSDYKVRILDGAAGT 486

Query: 476 ASSIRVLIESGDKESRWGTVGVSENIVDASYQALLDSVEYKL 517
           ++  RVL+ES +   RW TVGVS NI++ASYQA+++ +EY L
Sbjct: 487 SAKTRVLVESSNGSQRWSTVGVSGNIIEASYQAVVEGIEYGL 528


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: 701
Number of extensions: 17
Number of successful extensions: 3
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: 542
Length adjustment: 35
Effective length of query: 493
Effective length of database: 507
Effective search space:   249951
Effective search space used:   249951
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 Synpcc7942_0428 Synpcc7942_0428 (putative 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.25929.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-265  865.0   0.0   9.2e-265  864.7   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0428  Synpcc7942_0428 putative alpha-i


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0428  Synpcc7942_0428 putative alpha-isopropylmalate/homocitrate synthase family 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.7   0.0  9.2e-265  9.2e-265       2     521 ..       9     532 ..       8     536 .. 0.99

  Alignments for each domain:
  == domain 1  score: 864.7 bits;  conditional E-value: 9.2e-265
                                 TIGR00977   2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvva 70 
                                               + +ydttlrdGaq+eG+slsledk+ria+ ld lG+++ieGGwpganpkdv+ff+++++ +l++a+vva
  lcl|FitnessBrowser__SynE:Synpcc7942_0428   9 IAVYDTTLRDGAQREGLSLSLEDKLRIAHCLDRLGVKFIEGGWPGANPKDVQFFWELQQRPLQQAEVVA 77 
                                               78******************************************************************* PP

                                 TIGR00977  71 fsstrrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadevi 139
                                               f+strrp +   ed+ l+al+ a+t +vtifGkswdlhv e+lkt+l+enl mi+d+++yl+   ++vi
  lcl|FitnessBrowser__SynE:Synpcc7942_0428  78 FCSTRRPGQIAGEDELLKALLAAGTTWVTIFGKSWDLHVVEGLKTSLDENLVMISDSIAYLRTCDRRVI 146
                                               ********************************************************************* PP

                                 TIGR00977 140 ydaehffdGykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrl.......kdpql 201
                                               ydaeh+fdGy anp+yal+tl++a +aGa+w+vl+dtnGG lph+i+ei+  v  r+         pql
  lcl|FitnessBrowser__SynE:Synpcc7942_0428 147 YDAEHWFDGYLANPDYALQTLAAAIEAGAEWIVLCDTNGGCLPHQISEIVAAVLDRFpslapdqTGPQL 215
                                               *************************************************************99889*** PP

                                 TIGR00977 202 GihahndsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltev 270
                                               Gih+hndsetavan+++av+aGa++v+GtinG+GercGnanlcs+ipnlqlklg+d++e e+l +lt +
  lcl|FitnessBrowser__SynE:Synpcc7942_0428 216 GIHTHNDSETAVANAIAAVQAGARMVHGTINGYGERCGNANLCSVIPNLQLKLGYDCVETEQLMQLTAT 284
                                               ********************************************************************* PP

                                 TIGR00977 271 arlvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvle 339
                                               +rlv+eivnla+d+++ yvG+safahkGG+hvsav+rnp tyehi pe vGn r+iv+se++G+snvl 
  lcl|FitnessBrowser__SynE:Synpcc7942_0428 285 SRLVSEIVNLAPDDHAAYVGQSAFAHKGGIHVSAVERNPLTYEHIRPEQVGNLRRIVISEQSGLSNVLA 353
                                               ********************************************************************* PP

                                 TIGR00977 340 klkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrd 408
                                               k++ +G+++++++p++r++l+++kele qGy+feaaeas++ll+r+a G+r ++f+++ f+v++ k+r+
  lcl|FitnessBrowser__SynE:Synpcc7942_0428 354 KARSFGLDLQRNDPACRDLLARLKELESQGYQFEAAEASFDLLMREATGDRPHFFDLKDFHVHCSKQRQ 422
                                               ********************************************************************* PP

                                 TIGR00977 409 eeslseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsa 477
                                               e    +a+atv+v+v g ++l+ aeGnGpvsald alrka+  fyp + +++l dykvril+++aGtsa
  lcl|FitnessBrowser__SynE:Synpcc7942_0428 423 E---LNALATVKVAVTGRDILESAEGNGPVSALDAALRKAIGSFYPAVMQFHLSDYKVRILDGAAGTSA 488
                                               *...89*************************************************************** PP

                                 TIGR00977 478 ktrvliessdGkrrwgtvGvseniieasytallesieyklrkde 521
                                               ktrvl+ess+G +rw+tvGvs+niieasy+a++e+iey+l +++
  lcl|FitnessBrowser__SynE:Synpcc7942_0428 489 KTRVLVESSNGSQRWSTVGVSGNIIEASYQAVVEGIEYGLLLQQ 532
                                               ***************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (526 nodes)
Target sequences:                          1  (542 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.19
//
[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