GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Rhodococcus qingshengii djl-6-2

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_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

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



>NCBI__GCF_002893965.1:WP_050656086.1
          Length = 679

 Score =  366 bits (940), Expect = e-105
 Identities = 203/490 (41%), Positives = 294/490 (60%), Gaps = 7/490 (1%)

Query: 7   VLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNIE 66
           VLVANRGEIA RV++ ++E+G+ ++AVYS+AD  A H + AD A  IG A A +SYL I+
Sbjct: 10  VLVANRGEIAVRVIRTLRELGIRSVAVYSDADANARHVREADTAVNIGPAAARESYLVID 69

Query: 67  HIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLAN 126
            +IDAA+      IHPGYGFLSEN+ F+ A   AGI F+GPS   +  + DK+  K    
Sbjct: 70  KVIDAAKSTGAQGIHPGYGFLSENSAFSAACAAAGIAFLGPSEHAIEVMGDKITAKNSVA 129

Query: 127 MAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWERN 186
              VP  PG   P  + +E +  AE IGYP++VK ++GGGG G+  V++   L +     
Sbjct: 130 AFDVPVVPGIARPNLTDEELIAAAEDIGYPVLVKPSAGGGGKGMRLVEDPANLAEALRSA 189

Query: 187 KRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAPS 246
           +R A  +FG   LF+E++ + PRHIE Q++ D++GN V   EREC++QRR+QK+IEEAPS
Sbjct: 190 RREAASSFGDDTLFLERFVLRPRHIEVQVLADQHGNVVHLGERECSLQRRHQKVIEEAPS 249

Query: 247 PALKMEERESMFEPIIKFGKLINYFTLGTFETAFS-DVSRDFYFLELNKRLQVEHPTTEL 305
           P L    R+ +        + ++Y   GT E   S D   +F+F+E+N RLQVEHP TE+
Sbjct: 250 PLLDQVTRDRIGAAACNTARSVDYTGAGTVEFIVSADKPDEFFFMEMNTRLQVEHPVTEM 309

Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365
           +  +DLV+ Q+++AAGE L FSQ D+   + G AIE R+ AED    F  + G V    E
Sbjct: 310 VTGLDLVEWQVRVAAGEKLAFSQSDIT--LTGHAIEARVYAEDPGRGFLPTGGRVVDLVE 367

Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425
           P+G GVRVDSG+ +G+ V   YD ++SK+I +   R  A++   RAL D  + G+ T IE
Sbjct: 368 PSGSGVRVDSGLLAGTVVGSDYDPMLSKVIAHAPDRAGALRKLDRALGDTAVLGVVTNIE 427

Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLRTSSTDNK 485
             ++++ DPD   G   T  + ++ + FV      E + AA A     R L R ++++  
Sbjct: 428 FARFLLADPDVIAGNLDTGLLDRRVEDFVAADASDEVLIAAAA----YRWLSRWTTSERF 483

Query: 486 GKAQSKSGWK 495
                 SGW+
Sbjct: 484 DPWDVPSGWR 493


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: 671
Number of extensions: 26
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: 509
Length of database: 679
Length adjustment: 37
Effective length of query: 472
Effective length of database: 642
Effective search space:   303024
Effective search space used:   303024
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