GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Shewanella sp. ANA-3

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 7026296 Shewana3_3438 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)

Query= SwissProt::Q2QMG2
         (737 letters)



>FitnessBrowser__ANA3:7026296
          Length = 1517

 Score =  295 bits (756), Expect = 9e-84
 Identities = 176/459 (38%), Positives = 259/459 (56%), 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  INKVLVHARGCTAVKLIRKAHDNDINVVLVASDPDMTAVPADMLKDSDKLVCLGGNTSDE 999

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

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

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

Query: 276  IEEAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEH 335
            +EE+ +  +  + +  + +   +   A  Y  AGTVEFI +  + E YFMEMNTRLQVEH
Sbjct: 1180 VEESGSTMLPEELKKQVLDYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEH 1239

Query: 336  PVTEMIVGQDLVEWQIRIANGECLP-LSQEQVPLNGHAFEARIYAENVPRG------FLP 388
            PVTE   G D+V  Q  IA G  +  L  +++   G+A E R+ AE            +P
Sbjct: 1240 PVTEATSGIDIVSAQFDIAAGRSIENLEPKEI---GYAMEVRVTAEKAALDSHGVLQLIP 1296

Query: 389  ATGTLHHYRPVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSN 448
              G +      P    V + +    G  VS +YD +IA++++ GE+R   + KL   L +
Sbjct: 1297 NPGKITEC-VFPDHPDVEIISIAAAGKEVSPYYDSLIAQVIMRGENREDVIAKLHAYLDS 1355

Query: 449  FQIAGLPTNVGFLQELAGHSAFEKGLVDTHFIERYQNDL 487
              + G+ TN+  L+ +     F++G+ DT+++ R+  +L
Sbjct: 1356 VVLKGIATNIPLLKLILSDGTFKEGVYDTNYLPRFMAEL 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: 1850
Number of extensions: 66
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.

Links

Downloads

Related tools

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:

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