Alignments for a candidate for leuB in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Synechococcus elongatus PCC 7942

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate Synpcc7942_1505 Synpcc7942_1505 3-isopropylmalate dehydrogenase

Query= BRENDA::Q00412
         (355 letters)



>FitnessBrowser__SynE:Synpcc7942_1505
          Length = 365

 Score =  546 bits (1408), Expect = e-160
 Identities = 273/352 (77%), Positives = 302/352 (85%)

Query: 1   MTQNYRITLLSGDGIGPEIMAVAVDVLKAVGKQLDLNFEFKEALMGGVAIDATGEPLPEE 60
           MT++YRITLL GDGIGPEIMAV VD+L+A+G+Q DLNFEF+EAL+GG AIDATGEPLPE 
Sbjct: 1   MTRSYRITLLPGDGIGPEIMAVTVDILRAIGRQFDLNFEFEEALIGGSAIDATGEPLPEA 60

Query: 61  SLQACRDSDAVLLAAIGGYKWDNLPRPERPETGLLALRAGLGLFANRARLLFCPHVLDAS 120
           +L  CR+SDAVLLAAIGGYKWD+LPR +RPETGLL LRAGLGLFAN       P ++DAS
Sbjct: 61  TLATCRNSDAVLLAAIGGYKWDSLPRSQRPETGLLGLRAGLGLFANLRPAAILPQLVDAS 120

Query: 121 SLKREVVEGVDIMVVRELTGGIYFGQPKGIFETETGKNEGSNTMAYGESEIDRIGRVGFE 180
           SLKREV+EGVD+MVVRELTGGIYFG+PKG F  E G+    NTM Y E EIDRIGRV F+
Sbjct: 121 SLKREVIEGVDLMVVRELTGGIYFGEPKGCFADEQGRQRAFNTMVYREDEIDRIGRVAFD 180

Query: 181 TAKKRQGRLCSVDKANVLDVSQLWRDRIMALAADYPEVELSHLYVDNAAMQLVRWPKQFD 240
            A+KR  RLCSVDKANVL+VSQLWRDR+  L +DY +VELSHLYVDNAAMQLVRWPKQFD
Sbjct: 181 IARKRGKRLCSVDKANVLEVSQLWRDRMTLLGSDYADVELSHLYVDNAAMQLVRWPKQFD 240

Query: 241 TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGQDKANPLAQ 300
           TIVTGNLFGDILSD AAMLTGSIGMLPSASLGA GPGVFEPVHGSAPDIAGQDKANPLAQ
Sbjct: 241 TIVTGNLFGDILSDIAAMLTGSIGMLPSASLGAEGPGVFEPVHGSAPDIAGQDKANPLAQ 300

Query: 301 VLSAAMMLRYGLDEPAASDPVEKAVLKVLDWGYPTGDIMSEGMKAVGCRKWG 352
           VLSAAMMLRYGLDEP A+  +E AV +VLD GY TGD+ SEGM  VGC+  G
Sbjct: 301 VLSAAMMLRYGLDEPEAAARIEAAVNQVLDQGYRTGDLYSEGMTLVGCKGMG 352


Lambda     K      H
   0.318    0.137    0.407 

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: 517
Number of extensions: 21
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: 355
Length of database: 365
Length adjustment: 29
Effective length of query: 326
Effective length of database: 336
Effective search space:   109536
Effective search space used:   109536
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: 49 (23.5 bits)

Align candidate Synpcc7942_1505 Synpcc7942_1505 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.12081.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-162  524.6   0.0   6.2e-162  524.4   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1505  Synpcc7942_1505 3-isopropylmalat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1505  Synpcc7942_1505 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.4   0.0  6.2e-162  6.2e-162       1     348 [.       6     354 ..       6     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: 524.4 bits;  conditional E-value: 6.2e-162
                                 TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                               +i++LpGDgiGpe++a  +++L a+  +f+l++efeealiGG aidatgePlpe+tl++c+++davLl+
  lcl|FitnessBrowser__SynE:Synpcc7942_1505   6 RITLLPGDGIGPEIMAVTVDILRAIGRQFDLNFEFEEALIGGSAIDATGEPLPEATLATCRNSDAVLLA 74 
                                               699****************************************************************** PP

                                 TIGR00169  70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138
                                               a+GG+kWd+lpr++rPe+gLL lr  l+lfanLrPa + ++L+++s+lk+e+++gvDl+vvreLtgGiY
  lcl|FitnessBrowser__SynE:Synpcc7942_1505  75 AIGGYKWDSLPRSQRPETGLLGLRAGLGLFANLRPAAILPQLVDASSLKREVIEGVDLMVVRELTGGIY 143
                                               ********************************************************************* PP

                                 TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206
                                               fGepk+ + +e+ +++a++t++Y+++ei+ri rvaf +arkr k+++svDkanvLe+s+lWr++++ + 
  lcl|FitnessBrowser__SynE:Synpcc7942_1505 144 FGEPKGCFADEQgRQRAFNTMVYREDEIDRIGRVAFDIARKRGKRLCSVDKANVLEVSQLWRDRMTLLG 212
                                               *********99999******************************************************* PP

                                 TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275
                                                +y dvel+hly+DnaamqLv+ P+q+d++vt+nlfGDilsD+a+++tGs+G+LPsasl+ +g ++fep
  lcl|FitnessBrowser__SynE:Synpcc7942_1505 213 SDYADVELSHLYVDNAAMQLVRWPKQFDTIVTGNLFGDILSDIAAMLTGSIGMLPSASLGAEGPGVFEP 281
                                               ********************************************************************* PP

                                 TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344
                                               vhgsapdiag++ anp+a++lsaa++lry+l+ +eaa++ieaav++vl++g+rt dl+se+ t v++k 
  lcl|FitnessBrowser__SynE:Synpcc7942_1505 282 VHGSAPDIAGQDKANPLAQVLSAAMMLRYGLDEPEAAARIEAAVNQVLDQGYRTGDLYSEGMTLVGCKG 350
                                               ********************************************************************9 PP

                                 TIGR00169 345 veee 348
                                               +++ 
  lcl|FitnessBrowser__SynE:Synpcc7942_1505 351 MGDA 354
                                               9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (365 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: 00:00:00.01
# Mc/sec: 9.37
//
[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