Alignments for a candidate for leuB in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Desulfovibrio vulgaris Miyazaki F

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 8501058 DvMF_1794 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::P93832
         (405 letters)



>FitnessBrowser__Miya:8501058
          Length = 358

 Score =  414 bits (1065), Expect = e-120
 Identities = 219/354 (61%), Positives = 259/354 (73%), Gaps = 1/354 (0%)

Query: 45  ITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAK 104
           I L+PGDGIGPE+V  A  VL +     G   ++    IGGAA+D  G PLP+ET++A K
Sbjct: 5   ICLMPGDGIGPEIVEQAVKVLDKVAKKFGHTVSYTNALIGGAAIDATGGPLPDETVAACK 64

Query: 105 ESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREV 164
            +DAVLLGA+GG KWD     +RPEKGLL IR AL +FANLRPAT+LP+L  A  L+ ++
Sbjct: 65  AADAVLLGAVGGPKWDTLPTAIRPEKGLLGIRKALGLFANLRPATLLPELAGACLLRADI 124

Query: 165 A-EGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKR 223
           A +G+D+MVVRELTGG+YFGEP   +   +G    +NT +Y   E+ RIARVAFE ARKR
Sbjct: 125 AAQGLDVMVVRELTGGVYFGEPVCEEELRDGLRTSYNTMIYNEEEVRRIARVAFEAARKR 184

Query: 224 RGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTN 283
             K+CSVDKANVL  S LWR  V  +A EYPDVEL+HMYVDNAAMQLVR P QFD IVT 
Sbjct: 185 SRKVCSVDKANVLAVSRLWRAVVIEVAREYPDVELTHMYVDNAAMQLVRWPAQFDVIVTE 244

Query: 284 NIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAA 343
           N+FGDILSDEA++ITGSIGMLPSASL  SGPG+FEPIHGSAPDIAGQ+KANP+ATILS A
Sbjct: 245 NLFGDILSDEAAVITGSIGMLPSASLGASGPGIFEPIHGSAPDIAGQNKANPVATILSVA 304

Query: 344 MLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSV 397
           M+L+Y  G EK A  IE AV   L  G+RTGDI   G  LVG   MG  V + V
Sbjct: 305 MMLRYTFGLEKEAVAIEQAVSGVLREGYRTGDIMEEGKTLVGTVSMGNLVTERV 358


Lambda     K      H
   0.316    0.134    0.374 

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: 417
Number of extensions: 8
Number of successful extensions: 2
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: 405
Length of database: 358
Length adjustment: 30
Effective length of query: 375
Effective length of database: 328
Effective search space:   123000
Effective search space used:   123000
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: 50 (23.9 bits)

Align candidate 8501058 DvMF_1794 (3-isopropylmalate dehydrogenase (RefSeq))
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.24966.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-162  526.9   0.0   1.3e-162  526.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501058  DvMF_1794 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501058  DvMF_1794 3-isopropylmalate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.7   0.0  1.3e-162  1.3e-162       1     347 [.       4     352 ..       4     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 526.7 bits;  conditional E-value: 1.3e-162
                         TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 
                                       ki ++pGDgiGpe+v++a+kvL++v+++f++ + + +aliGGaaidatg Plp+et++ack+adavLlgavGGpkWd
  lcl|FitnessBrowser__Miya:8501058   4 KICLMPGDGIGPEIVEQAVKVLDKVAKKFGHTVSYTNALIGGAAIDATGGPLPDETVAACKAADAVLLGAVGGPKWD 80 
                                       799************************************************************************** PP

                         TIGR00169  78 nlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaee.ek 152
                                       +lp+ +rPekgLL +rk l+lfanLrPa+l ++L  ++ l+++i+ +g+D++vvreLtgG+YfGep  +ee  +  +
  lcl|FitnessBrowser__Miya:8501058  81 TLPTAIRPEKGLLGIRKALGLFANLRPATLLPELAGACLLRADIAaQGLDVMVVRELTGGVYFGEPVCEEELRDgLR 157
                                       ********************************************989*******************99988777799 PP

                         TIGR00169 153 kaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvks 229
                                       ++++t+ Y++ee++riarvafe+arkr +kv+svDkanvL++srlWr +v e+a+eyPdvel h+y+DnaamqLv+ 
  lcl|FitnessBrowser__Miya:8501058 158 TSYNTMIYNEEEVRRIARVAFEAARKRSRKVCSVDKANVLAVSRLWRAVVIEVAREYPDVELTHMYVDNAAMQLVRW 234
                                       9**************************************************************************** PP

                         TIGR00169 230 PeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllrysl 306
                                       P+q+dv+vt+nlfGDilsDea+vitGs+G+LPsasl+ +g ++fep+hgsapdiag++ anp+a+ils+a++lry++
  lcl|FitnessBrowser__Miya:8501058 235 PAQFDVIVTENLFGDILSDEAAVITGSIGMLPSASLGASGPGIFEPIHGSAPDIAGQNKANPVATILSVAMMLRYTF 311
                                       ***************************************************************************** PP

                         TIGR00169 307 nleeaaeaieaavkkvleegkrtedlaseattavstkevee 347
                                       +le++a aie+av+ vl+eg+rt d+++e+ t v+t ++++
  lcl|FitnessBrowser__Miya:8501058 312 GLEKEAVAIEQAVSGVLREGYRTGDIMEEGKTLVGTVSMGN 352
                                       **********************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (358 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.43
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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