GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Brevibacterium jeotgali SJ5-8

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 WP_101586891.1 BJEO58_RS00855 acetyl/propionyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_900169175.1:WP_101586891.1
          Length = 699

 Score =  343 bits (879), Expect = 2e-98
 Identities = 188/496 (37%), Positives = 287/496 (57%), Gaps = 6/496 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+R+L+ANRGEIA RV++  + +G+  +AVYS+AD  A HT+ AD A+ +G APA  SYL
Sbjct: 2   FTRILIANRGEIALRVIRTCRALGIETVAVYSDADADAAHTRAADVAHRLGPAPAAQSYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           +IE ++ A       A+HPGYGFLSENA FA  +E+ GI F+GP++  +  + DK+  KR
Sbjct: 62  DIERVVAAVRATGAQAVHPGYGFLSENAAFARRLEEEGIVFLGPTAASIDVMGDKISAKR 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
                GVP  PG   P  + ++ +  A+++G+PI+VK ++GGGG G+  V +   L +  
Sbjct: 122 AVAARGVPLVPGVAEPGLTDEQLIARADEVGFPILVKPSAGGGGKGMREVHDPADLAEAL 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              +R A  +FG   LF+E+  + PRHIE Q++ D++GN +   EREC++QRR+QK+IEE
Sbjct: 182 ASARREAAGSFGDDTLFLERLVLTPRHIEVQVLADEHGNVIHLGERECSLQRRHQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFS-DVSRDFYFLELNKRLQVEHPT 302
           APS  L    R  + +  +   K ++Y   GT E   S D   +F+F+E+N RLQVEHP 
Sbjct: 242 APSALLDEATRARIGQAAVDTAKSVDYRGAGTVEFIVSADNPDEFFFMEMNTRLQVEHPV 301

Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362
           TE +  +DLV+ Q+++ AG+ L  +Q+D+   + G +IE RI AED    F  + G    
Sbjct: 302 TEQVTGVDLVEWQLRIGAGQQLALAQDDVT--LTGHSIEARIYAEDPARGFLPTGGTALD 359

Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
              PTG G+RVD+G+E G  +   YD +++KLIV    R+ A+     ALA   + GI T
Sbjct: 360 VSFPTGEGIRVDAGLEPGQRIVSDYDPMIAKLIVTARDRQEAVARTRTALAGSAVPGIVT 419

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAA---IAAEIQSRGLLRT 479
            I   + +++ P+   G   T  I   T+  +    +   ++ A   +AA    R     
Sbjct: 420 NIGFLQTLLEMPEVVAGDLHTGLIDAMTEDDLAEAVDPAALQLAAAHVAAAEADRATDSH 479

Query: 480 SSTDNKGKAQSKSGWK 495
            + +  G     SGW+
Sbjct: 480 IAGEPVGMWADGSGWR 495


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: 742
Number of extensions: 33
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: 509
Length of database: 699
Length adjustment: 37
Effective length of query: 472
Effective length of database: 662
Effective search space:   312464
Effective search space used:   312464
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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