GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuB in Shewanella amazonensis SB2B

Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate 6936392 Sama_0580 acetyl-CoA carboxylase multifunctional enzyme accADC, carboxyl transferase subunit alpha/carboxyl transferase subunit beta/biotin carboxylase (RefSeq)

Query= SwissProt::Q2QMG2
         (737 letters)



>lcl|FitnessBrowser__SB2B:6936392 Sama_0580 acetyl-CoA carboxylase
            multifunctional enzyme accADC, carboxyl transferase
            subunit alpha/carboxyl transferase subunit beta/biotin
            carboxylase (RefSeq)
          Length = 1517

 Score =  305 bits (782), Expect = 9e-87
 Identities = 182/459 (39%), Positives = 263/459 (57%), Gaps = 14/459 (3%)

Query: 39   VEKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALH---VRAADEAVRLGPPPARE 95
            ++KVLV  RG  A +++R A    I  V V SD D  A+    ++  D+ V LG   + E
Sbjct: 940  IDKVLVHARGCTAVKLIRKAHDNNINVVLVASDPDMTAVPADMLKENDKLVCLGGNTSDE 999

Query: 96   SYLNASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSA 155
            SYLNA +++  A      A+HPG GFLSES  FA LC   G+ F+GP   ++  MG+KS 
Sbjct: 1000 SYLNAYSVLKVAEYENVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNKSN 1059

Query: 156  SKRIMGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFV 215
            + +   A  VP+VPG HG   + E     A++IGYPVL+K   GGGGKG+++V+RPED +
Sbjct: 1060 AIKTSQAQNVPVVPGSHGILSNAEQAVNVASEIGYPVLLKAVQGGGGKGIQVVKRPEDMI 1119

Query: 216  DSVLSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKI 275
               +    EAAA+FG   L +EKY+T  RHIEVQ+  D+ GN   L  RDCS+QR +QK+
Sbjct: 1120 PLFMKTSTEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGNAKVLGLRDCSVQRNNQKV 1179

Query: 276  IEEAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEH 335
            IEE+ +  +  + +  +     S   AV Y  AGTVEFI +  + E YFMEMNTRLQVEH
Sbjct: 1180 IEESGSTMLPPELKQQVMAYTKSLGDAVDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEH 1239

Query: 336  PVTEMIVGQDLVEWQIRIANGECL-PLSQEQVPLNGHAFEARIYAE------NVPRGFLP 388
            PVTE   G D+V  Q  IA G  +  L  +++   G+A E R+ AE      N     +P
Sbjct: 1240 PVTEATSGIDIVSAQFDIAAGRSIEDLEPQEI---GYAMEVRVTAEKAALDSNGVLQLVP 1296

Query: 389  ATGTLHHYRPVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSN 448
              G +     +P    V + +   EG  VS +YD +IA++++ GESR   + K+ + L +
Sbjct: 1297 NPGKITEC-VMPERDDVEIISIAAEGKEVSPYYDSLIAQIIIRGESREDVVTKMYDYLDS 1355

Query: 449  FQIAGLPTNVGFLQELAGHSAFEKGLVDTHFIERYQNDL 487
              I G+ TN+  L+ +   + F +G+ DT+++ R   +L
Sbjct: 1356 VVIKGIATNIPLLKRILKDATFNEGVYDTNYLPRLMAEL 1394


Lambda     K      H
   0.317    0.133    0.389 

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: 1839
Number of extensions: 78
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: 737
Length of database: 1517
Length adjustment: 45
Effective length of query: 692
Effective length of database: 1472
Effective search space:  1018624
Effective search space used:  1018624
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: 58 (26.9 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:

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:

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:

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.

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