Alignments for a candidate for bkdC in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for bkdC in Shewanella loihica PV-4

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 5211004 Shew_3430 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase (RefSeq)

Query= reanno::Smeli:SMc03203
         (426 letters)



>FitnessBrowser__PV4:5211004
          Length = 650

 Score =  249 bits (635), Expect = 2e-70
 Identities = 163/437 (37%), Positives = 237/437 (54%), Gaps = 43/437 (9%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I +PD+G+  ++ +++E  V  GD +  D  L  + TDKAT+E+P+P  GK++ +  +VG
Sbjct: 223 ISVPDIGDA-SDVDVIEVLVAAGDVIEADQGLITLETDKATMEVPAPFAGKLVSVTVKVG 281

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V+  + +  IET   A  AAP     A A      PVA     +A AP     PA   
Sbjct: 282 DKVSQGSVIATIETQSSAPVAAPAPAAAAPA------PVA-----QASAPA----PAASK 326

Query: 126 APAPREAPDLSAKPL-----ASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFI--- 177
            P P   P   +KP+     ASPAVR  ARE G DL QV GTGP GRI  ED+  FI   
Sbjct: 327 PPVPHH-PSAGSKPVTGAVHASPAVRRLAREFGADLTQVTGTGPKGRILKEDVQAFIKYE 385

Query: 178 -----SRGAEPLPAQTGLVRKTA-----------VEEVRMIGLRRRIAEKMSLSTSRIPH 221
                +  A  + A  G ++  A           VEEV +  +++     +  +   IPH
Sbjct: 386 LSRPKASAATSVGAGEGGLQVIAAPKVDFAKFGEVEEVPLSRIQKISGPNLHRNWVTIPH 445

Query: 222 ITYVEEVDMTALEDLRATMNRDRKPEQA--KLTILPFLMRALVKTVAEQPGVNATFDDHA 279
           +T  +E D+T +E  R   N     ++   K+T L F+M+A+ KT+ + P  NA+     
Sbjct: 446 VTQFDEADITEMEAFRKQQNEIAAKQKTGVKITPLVFMMKAVAKTLQQFPVFNASLSADG 505

Query: 280 GVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTG 339
             + +    HIG+A  TP GL VPVVR  + +GI + +AEL  ++  AR G     ++ G
Sbjct: 506 ESLIKKKYYHIGVAVDTPNGLVVPVVRDVDKKGIIELSAELMEISVKARDGKLKAADMQG 565

Query: 340 STITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRV 399
           S  TISSLG IGG A TP++N+P+VAI+GV+K  ++P W+G +F P+ ++ LS S+DHRV
Sbjct: 566 SCFTISSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRV 625

Query: 400 IDGWDAAVFVQRLKTLL 416
           IDG  AA F   L ++L
Sbjct: 626 IDGAMAARFSVTLSSML 642



 Score = 57.8 bits (138), Expect = 1e-12
 Identities = 37/114 (32%), Positives = 62/114 (54%), Gaps = 4/114 (3%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G+  ++ +++E  V  GD +  D  L  + TDKAT+E+P+P  G V  +   VG
Sbjct: 118 VTVPDIGDA-SDVDVIEVLVAVGDSINVDTGLITLETDKATMEVPAPAAGVVKEMKVAVG 176

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPE 119
           D V+  + ++ +E +G  GEAA  +   A A      P A +S +E K    P+
Sbjct: 177 DKVSQGSLVLMLEVSG--GEAAAPAASAAPAPSAEAAPAAAAS-IEVKEISVPD 227



 Score = 53.9 bits (128), Expect = 1e-11
 Identities = 40/121 (33%), Positives = 60/121 (49%), Gaps = 14/121 (11%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G    E +++E     GD +  +  +  V +DKAT++IP+P  GK+  +   VG
Sbjct: 7   VLVPDIGGD--EVQVIEICAAVGDTLAAEESIITVESDKATMDIPAPFAGKLAEIKVAVG 64

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           DTV+ +  L+ +  AGEA  A P     A        PVA  +   A AP  P   AP  
Sbjct: 65  DTVS-EGTLIAMMEAGEAQAAEPAPAESA--------PVAAPA---APAPAAPVASAPAS 112

Query: 126 A 126
           A
Sbjct: 113 A 113


Lambda     K      H
   0.317    0.133    0.384 

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: 702
Number of extensions: 34
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 426
Length of database: 650
Length adjustment: 35
Effective length of query: 391
Effective length of database: 615
Effective search space:   240465
Effective search space used:   240465
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources