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

GapMind for catabolism of small carbon sources

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

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_076948772.1 C1M55_RS06175 ATP-grasp domain-containing protein

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_002893965.1:WP_076948772.1
          Length = 655

 Score =  366 bits (940), Expect = e-105
 Identities = 240/687 (34%), Positives = 359/687 (52%), Gaps = 52/687 (7%)

Query: 4   KILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSYIVI 63
           ++LIANRGEI  R+ +TAR++G+S V I S  D  A   ++AD  V +     ++SY   
Sbjct: 3   RLLIANRGEIVTRIARTARRLGMSVVTISSPVDSHAQWHRLADHTVLLDGDIPSESYTNS 62

Query: 64  DKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSKKIA 123
           D+++AA  A    AVHPGYGFLSE+S FAEA+ A G+ FVGP   +I  +GDK  +KK A
Sbjct: 63  DQIIAAALAADCDAVHPGYGFLSEDSDFAEAVVAAGLTFVGPAAESIALLGDKARAKKAA 122

Query: 124 QEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREGFQS 183
            +A + T+  +     D D  +     +  PV++K   GGGGKGM       +ARE   S
Sbjct: 123 ADAGIPTLTAWGEASADPDTVLGHVRSLDVPVLLKPVFGGGGKGMVRLHPGDDAREVITS 182

Query: 184 SKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVEEAP 243
           +      +FG   + IE  V +PRHIE+QVL DS G G++   RECS+QRRNQK++E+AP
Sbjct: 183 AIGLNERNFGRGDLMIETLVERPRHIEVQVLFDSFGTGVHFFTRECSLQRRNQKIIEQAP 242

Query: 244 SPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTELI 303
           +  + E+   AM   A+ L   VGY +A TVEF+VD +  +YFLE+NTRLQVEH VTE +
Sbjct: 243 ASSVPESVLGAMQHDALRLLGGVGYVNAATVEFLVDAENRYYFLEVNTRLQVEHTVTEEV 302

Query: 304 TGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRPPAE 363
           TGVDLVE  + +A G  L + Q  + L G+A++ R+YAEDP  GF P+         P+ 
Sbjct: 303 TGVDLVELQLDIALGARLPLQQRHIALRGFAVQARIYAEDPSNGFRPA---------PSH 353

Query: 364 TAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAIEAM 423
           +      V+  W    PSG   VR D+     G I  +YDPMIAK+    PTR+ A+E++
Sbjct: 354 S------VDIAW----PSG---VRIDSAFEGAGSIPPFYDPMIAKVIASGPTRSTALESL 400

Query: 424 RIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLRRVA 483
             AL      G   N+ FL  ++  P   + D+ T+F+ E          +P++   +  
Sbjct: 401 DRALTDSSYFGGTSNIGFLRLLLATPAVRADDIHTSFVDEHLTR-----LIPDSAELQAT 455

Query: 484 AAAAAMHRVAEIRRTRVSGRM--------DNHERRVGTEWVVTLQGAD---FPVTIAADH 532
           AAA AM   +   ++ V+G              R++G++ +     AD    P T+ +  
Sbjct: 456 AAAVAMVWTSVEEQSPVTGSSWTGPHGLHRETLRKLGSDPIGRELIADARVVPTTVISQR 515

Query: 533 DGSTVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKV--H 590
               +   DG ++ V       +   +L+ DG         +  G  +   G  +KV   
Sbjct: 516 SNHWIVAADGRNISVVVRGGTDEVTLSLVADGLTTTAGRLGVGTGTWVCVGGWTVKVDEK 575

Query: 591 VRTPRQAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMEN 650
           V T + ++L           +   +   MPG ++ V ++ G  V EG  +  +EAMKME 
Sbjct: 576 VYTAKDSDL-----------SDGEITSKMPGTVLAV-LQTGTRVSEGDVVAVVEAMKMET 623

Query: 651 ILRAEKKGVVAKINASAGNSLAVDDVI 677
            LRA   G+V+ +  + G+ +    V+
Sbjct: 624 ALRASSPGIVSAVTVTVGDVIDAGQVL 650


Lambda     K      H
   0.317    0.134    0.387 

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: 964
Number of extensions: 34
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: 681
Length of database: 655
Length adjustment: 38
Effective length of query: 643
Effective length of database: 617
Effective search space:   396731
Effective search space used:   396731
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources