Alignments for a candidate for pccA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Shewanella loihica PV-4

Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 5210129 Shew_2573 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)

Query= BRENDA::Q19842
         (724 letters)



>FitnessBrowser__PV4:5210129
          Length = 677

 Score =  494 bits (1272), Expect = e-144
 Identities = 279/687 (40%), Positives = 421/687 (61%), Gaps = 29/687 (4%)

Query: 49  FDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYL 108
           F K+LIANRGEIACR+IKTA+ MGIKTVA++SD D ++ HV MADE+  +G +  ++SYL
Sbjct: 2   FTKLLIANRGEIACRIIKTAQVMGIKTVALYSDADKDARHVAMADESFYLGGSAPSESYL 61

Query: 109 RADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKK 168
           + + IL+  + +GAQA+HPGYGFLSEN  FA + E+AG  F+GP++ AI  MG K  +K 
Sbjct: 62  KGELILEIAKRSGAQAIHPGYGFLSENADFARQCEQAGIAFVGPSADAIDAMGSKSAAKI 121

Query: 169 IATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGY 228
           I   A V ++PGY G+   +++ +K S++IG+P +IKA+ GGGGKGMR+  ++ +A E  
Sbjct: 122 IMEQANVPLVPGYHGDDQSDEVLLKASKEIGFPQLIKAAYGGGGKGMRIVESESEALEAI 181

Query: 229 RLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEE 288
             +++EAASSFG+D++L+E+++  PRH+E+QV  D  GN ++L++R+CSIQRR+QKV+EE
Sbjct: 182 NSARREAASSFGNDKLLIERYLRQPRHVEVQVFADTQGNCIYLSDRDCSIQRRHQKVVEE 241

Query: 289 APSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDS-----QRNFYFLEMNTRLQVE 343
           AP+  +   +RR MGE AV  AKA+ Y  AGTVEFL+D+       +FYF+EMNTRLQVE
Sbjct: 242 APAPGLSDSLRRAMGEAAVAAAKAIDYVGAGTVEFLLDTHATEESNSFYFMEMNTRLQVE 301

Query: 344 HPITECITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRL 403
           HP+TE +TG D+V+  L V+ G  LP++QE V ++G +FE R+YAEDP   F LP+ G+L
Sbjct: 302 HPVTEMVTGQDLVKWQLMVASGSELPLSQEDVRIHGHSFEVRIYAEDPQNEF-LPASGKL 360

Query: 404 SRYVEPKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRG 463
           +   EP+    VR DSGIRE   IS +YDP+I KL+   ++R +AL R+  AL++Y I G
Sbjct: 361 NFLREPEQNRYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISG 420

Query: 464 VTHNIPLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSL---SPKEQDVVIAFASALNA 520
           + HNI  L +I + K F   D +T ++ E Y +   G +L   +  EQ+  +AFA+  + 
Sbjct: 421 LKHNIEFLANIAEHKAFSQADFSTDFI-ERYGDTLIGANLDGDNSHEQNGALAFAALYHL 479

Query: 521 RKLARANQFLNQNKQRS----THVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSAN 576
                  +    N Q        V+ F      +  L + + E   +H      +    +
Sbjct: 480 CAQKEQAKLTATNSQDPYSPWGQVSGFRLNRSGMHQLSLLDDEHEVQHLT----LSQIGD 535

Query: 577 KAQVRIGGKTVTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLP 636
              + +  + +T+SG+  L   +   E++G H +   V +   + T+      +  + L 
Sbjct: 536 CYYLNLNDQQLTLSGE--LKQDLLHAEING-HKSKIPVSREGDDFTLFLPSGSYHFRALQ 592

Query: 637 EQAVKYLQYMKEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLH 696
            + V+     ++K K        +PM G I    V+ GD V  GQ L+VMEAMKM+ ++ 
Sbjct: 593 TEVVEEQANSEDKLK--------APMNGTIVTHLVEVGDEVEAGQGLMVMEAMKMEYTIE 644

Query: 697 AGKTGRVKAVNVKVGATVDEGEVLVEL 723
           A   G V A   + G  V +G +L+E+
Sbjct: 645 APFDGTVAAFFFQPGELVSDGALLLEV 671


Lambda     K      H
   0.316    0.133    0.378 

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: 1093
Number of extensions: 54
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 724
Length of database: 677
Length adjustment: 39
Effective length of query: 685
Effective length of database: 638
Effective search space:   437030
Effective search space used:   437030
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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