GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_06283 H281DRAFT_06283 biotin carboxylase

Query= SwissProt::Q2QMG2
         (737 letters)



>FitnessBrowser__Burk376:H281DRAFT_06283
          Length = 455

 Score =  402 bits (1034), Expect = e-116
 Identities = 212/444 (47%), Positives = 289/444 (65%), Gaps = 7/444 (1%)

Query: 40  EKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARESYLN 99
           EK+L+ANRGEIA R+ R  R LG+ TV VYS+AD+ A +V+ ADEAV +GP P+  SYLN
Sbjct: 3   EKILIANRGEIALRIQRACRELGVKTVVVYSEADKEAKYVKLADEAVCIGPAPSNLSYLN 62

Query: 100 ASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSASKRI 159
             A++ AA  T A+AIHPGYGFLSE+ADFA+  +  G TFIGP P  IR MGDK  +K+ 
Sbjct: 63  MPALISAAEVTDAEAIHPGYGFLSENADFAERVEQSGFTFIGPRPETIRMMGDKVTAKQT 122

Query: 160 MGAAGVPLVPGYHGA--EQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFVDS 217
           M   GVP VPG  GA  E   E++K+ A ++GYPV+IK   GGGG+GMR+V      V++
Sbjct: 123 MIKTGVPCVPGSEGALPEDPKEIVKI-ARQVGYPVIIKAAGGGGGRGMRVVHTEAALVNA 181

Query: 218 VLSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKIIE 277
           V   + EA  +FG   + +EK++  PRHIE+Q+  D   N + L ERDCS+QRRHQK+IE
Sbjct: 182 VNMTREEAGRAFGNPQVYMEKFLENPRHIEIQVLSDSFKNAVWLGERDCSMQRRHQKVIE 241

Query: 278 EAPAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEHPV 337
           EAPAP +  +    IG+    A K +GY  AGT EF+ +  +GEFYF+EMNTR+QVEHPV
Sbjct: 242 EAPAPGIARRLIDRIGDRCADACKKMGYLGAGTFEFLYE--NGEFYFIEMNTRVQVEHPV 299

Query: 338 TEMIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHHYR 397
           TE+I G D+V+ QIRIA GE L   Q  +   GHA E RI AE+ P  F+P+ G L  + 
Sbjct: 300 TELITGVDIVQEQIRIAAGEKLAFRQRDIVFKGHAIECRINAED-PFKFIPSPGRLTSWH 358

Query: 398 PVPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIAGLPTN 457
            +P    +RV++    G  V  +YD MI KL+ +G +R  A+ +++ +LS   + G+ TN
Sbjct: 359 -MPGGPGIRVDSHAYNGYFVPPNYDSMIGKLIAYGATREQAIKRMRIALSEMVVEGIQTN 417

Query: 458 VGFLQELAGHSAFEKGLVDTHFIE 481
           +   +EL   + F +G    H++E
Sbjct: 418 IPLHRELMLDAKFVEGGTSIHYLE 441


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: 746
Number of extensions: 35
Number of successful extensions: 4
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: 455
Length adjustment: 36
Effective length of query: 701
Effective length of database: 419
Effective search space:   293719
Effective search space used:   293719
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: 53 (25.0 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:

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