Alignments for a candidate for pccA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Phaeobacter inhibens BS107

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate GFF2122 PGA1_c21540 propionyl-CoA carboxylase alpha chain

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Phaeo:GFF2122
          Length = 681

 Score = 1201 bits (3106), Expect = 0.0
 Identities = 601/681 (88%), Positives = 635/681 (93%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF KILIANRGEIACRVIKTARKMGI TVAIYSDADKQ+LHV+MADEAVHIGPPPANQSY
Sbjct: 1   MFEKILIANRGEIACRVIKTARKMGIKTVAIYSDADKQSLHVKMADEAVHIGPPPANQSY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           IVIDKVM AIRATGAQAVHPGYGFLSEN+KFAEAL AEGV FVGPP GAIE+MGDKITSK
Sbjct: 61  IVIDKVMEAIRATGAQAVHPGYGFLSENAKFAEALAAEGVAFVGPPVGAIESMGDKITSK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
           KIAQEA VSTVPGYMGLI DADEAVKISN+IGYPVMIKASAGGGGKGMRIAW+D EAREG
Sbjct: 121 KIAQEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSDAEAREG 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCD+HGNGIYLGERECSIQRRNQKVVE
Sbjct: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDAHGNGIYLGERECSIQRRNQKVVE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSPFLDE TRRAMGEQAVALAKAVGYASAGTVEFIVDG KNFYFLEMNTRLQVEHPVT
Sbjct: 241 EAPSPFLDEDTRRAMGEQAVALAKAVGYASAGTVEFIVDGDKNFYFLEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           ELITGVDLVEQMIR+A GEPLSITQ DVKL GWAIENRLYAEDPYRGFLPSIGRLTRYRP
Sbjct: 301 ELITGVDLVEQMIRIAGGEPLSITQNDVKLNGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           PAE AAGPL  +GKWQGDAP+GE AVRNDTGV+EGGEISMYYDPMIAKLCTW PTR AAI
Sbjct: 361 PAEVAAGPLHDSGKWQGDAPAGELAVRNDTGVFEGGEISMYYDPMIAKLCTWGPTRDAAI 420

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
            AMR ALD FEVEGIGHNLPFLSAVMDHP FI+G MTTAFI E+YPEGF GV LPE DLR
Sbjct: 421 AAMRDALDGFEVEGIGHNLPFLSAVMDHPIFIAGTMTTAFIEEQYPEGFNGVELPEQDLR 480

Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVSFD 540
           ++AAA+AAMHRVAEIRRTRVSGRMDNHER+VG++WVVTLQ   F VT+ AD DGSTV FD
Sbjct: 481 KIAAASAAMHRVAEIRRTRVSGRMDNHERKVGSDWVVTLQDVSFNVTVDADRDGSTVRFD 540

Query: 541 DGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPRQAELA 600
           DGS++RV SDWTPGDQLA L V    LV+KVGKISGGFRIR+RGADLKVHVRTPRQAELA
Sbjct: 541 DGSALRVASDWTPGDQLARLTVGDDSLVVKVGKISGGFRIRSRGADLKVHVRTPRQAELA 600

Query: 601 RLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVV 660
           +LMPEK+ PDTSK+LLCPMPGL+VK++VEVG EVQEGQALCTIEAMKMENILRAEKKGVV
Sbjct: 601 KLMPEKIAPDTSKLLLCPMPGLVVKLEVEVGDEVQEGQALCTIEAMKMENILRAEKKGVV 660

Query: 661 AKINASAGNSLAVDDVIMEFE 681
           + INA+AG+SLAVD+VIMEFE
Sbjct: 661 SAINAAAGDSLAVDEVIMEFE 681


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: 1455
Number of extensions: 43
Number of successful extensions: 1
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: 681
Length adjustment: 39
Effective length of query: 642
Effective length of database: 642
Effective search space:   412164
Effective search space used:   412164
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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