GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Paraburkholderia bryophila 376MFSha3.1

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate H281DRAFT_06283 H281DRAFT_06283 biotin carboxylase

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Burk376:H281DRAFT_06283
          Length = 455

 Score =  383 bits (983), Expect = e-111
 Identities = 205/447 (45%), Positives = 290/447 (64%), Gaps = 6/447 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F ++L+ANRGEIA R+ +A +E+G+  + VYSEADK A + K ADEA  IG AP+  SYL
Sbjct: 2   FEKILIANRGEIALRIQRACRELGVKTVVVYSEADKEAKYVKLADEAVCIGPAPSNLSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           N+  +I AAE    +AIHPGYGFLSENA+FAE VE++G TFIGP  E +R + DK+  K+
Sbjct: 62  NMPALISAAEVTDAEAIHPGYGFLSENADFAERVEQSGFTFIGPRPETIRMMGDKVTAKQ 121

Query: 124 LANMAGVPTAPGSDGPV-TSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182
                GVP  PGS+G +     E +K+A ++GYP+++KAA GGGG G+  V  +  L++ 
Sbjct: 122 TMIKTGVPCVPGSEGALPEDPKEIVKIARQVGYPVIIKAAGGGGGRGMRVVHTEAALVNA 181

Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242
               +  A +AFG   +++EK+  NPRHIE Q++ D + N V   ER+C++QRR+QK+IE
Sbjct: 182 VNMTREEAGRAFGNPQVYMEKFLENPRHIEIQVLSDSFKNAVWLGERDCSMQRRHQKVIE 241

Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302
           EAP+P +     + + +      K + Y   GTFE  +   + +FYF+E+N R+QVEHP 
Sbjct: 242 EAPAPGIARRLIDRIGDRCADACKKMGYLGAGTFEFLYE--NGEFYFIEMNTRVQVEHPV 299

Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362
           TELI  +D+V+ QI++AAGE L F Q D+    +G AIE RINAED    F  S G +T 
Sbjct: 300 TELITGVDIVQEQIRIAAGEKLAFRQRDI--VFKGHAIECRINAEDPF-KFIPSPGRLTS 356

Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
           +  P GPG+RVDS   +G +VPP YDS++ KLI YG +RE AI+    AL++  + GI+T
Sbjct: 357 WHMPGGPGIRVDSHAYNGYFVPPNYDSMIGKLIAYGATREQAIKRMRIALSEMVVEGIQT 416

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQK 449
            I L++ +M D  F EG  S  Y+  +
Sbjct: 417 NIPLHRELMLDAKFVEGGTSIHYLENR 443


Lambda     K      H
   0.317    0.135    0.385 

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: 575
Number of extensions: 24
Number of successful extensions: 5
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: 509
Length of database: 455
Length adjustment: 34
Effective length of query: 475
Effective length of database: 421
Effective search space:   199975
Effective search space used:   199975
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: 51 (24.3 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