Alignments for a candidate for pccA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Stenotrophomonas chelatiphaga DSM 21508

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_057507601.1 ABB28_RS05090 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Dino:3607308
         (681 letters)



>NCBI__GCF_001431535.1:WP_057507601.1
          Length = 660

 Score =  511 bits (1317), Expect = e-149
 Identities = 306/691 (44%), Positives = 394/691 (57%), Gaps = 43/691 (6%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MF KILIANRGEIACRVI T R++GI TVA+YSDADR A HVR+ADEA+ IGP+PA +SY
Sbjct: 1   MFTKILIANRGEIACRVIATCRRLGIATVAVYSDADRTARHVRLADEAIAIGPAPAAESY 60

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           +  D +++A R++GA+A+HPGYGFLSEN  FAEA    GV FIGPPA+AI AMGDK  +K
Sbjct: 61  LRADVILEAARRSGAQAIHPGYGFLSENAAFAEACAAAGVVFIGPPASAIRAMGDKSAAK 120

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
            + Q+A V   PGY G   D       +  IGYPV+IKASAGGGGKGMR   + A   E 
Sbjct: 121 ALMQQAGVPLTPGYHGDDQDPQFLRGQADAIGYPVLIKASAGGGGKGMRRVDDSAAFIEA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
             S + EA ++FG+D + +EK+V +PRHIEIQV  D HGN ++L ER+CS+QRR+QKV+E
Sbjct: 181 LASCQREARSAFGNDHVLVEKYVLRPRHIEIQVFGDGHGNVVHLFERDCSVQRRHQKVLE 240

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300
           EAP+P +    R AMG+ +   A+AVGY  AGTVEFI   D +FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGMTAERRAAMGKAAVDAARAVGYVGAGTVEFIASPDGDFYFMEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360
           E ITG DLV   +RVAAG+ LP  QD++ + G A+E RLYAED  + FLPSIG L   R 
Sbjct: 301 EFITGTDLVAWQLRVAAGQPLPKRQDELAIGGHALEARLYAEDADKGFLPSIGTLRHLRL 360

Query: 361 PVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAI 420
           P E A                    VR DTGV +G  I+ +YDPMIAKL  W  DR AA+
Sbjct: 361 PPESA-------------------HVRVDTGVEQGDTITPFYDPMIAKLIVWDVDRDAAL 401

Query: 421 EAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLT 480
             M+ AL   +V G+  N  F+  ++    F + ++ TA I E+  D       G A L 
Sbjct: 402 RRMQQALADCQVVGVTTNAGFLRRLVGTDSFAQAKLDTALI-EREQDALAAPAAGEAALW 460

Query: 481 RLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARF----------DVTIDA 530
            LAA  A    V    R  +              W + A  +R            + +  
Sbjct: 461 TLAAIGA----VVTTARAAVDARDPRSPWQAQDGWRIGASASRLLPLQQGERQHSLRVQT 516

Query: 531 DPGGSTVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVH 590
            PGG  V+     A +V+ R+  G     V +DG    + V +      +       +  
Sbjct: 517 QPGGWQVQRDAEPAQQVSGRFADGQ--LDVALDGQRWRVGVQRDDGQVYLFTAQGQQRFS 574

Query: 591 VRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMEN 650
           V  P          E+   D    LL PMPG +V   VE G +V  G  L  +EAMKME+
Sbjct: 575 VHDPVGES------EQATADAGS-LLAPMPGRIVATLVEPGSKVSRGTPLVVLEAMKMEH 627

Query: 651 ILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681
            L A    TV    A AG+ +    V+++FE
Sbjct: 628 TLAAPADGTVHGYRAKAGEQVGDGAVLVDFE 658


Lambda     K      H
   0.318    0.134    0.392 

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: 1188
Number of extensions: 60
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: 681
Length of database: 660
Length adjustment: 39
Effective length of query: 642
Effective length of database: 621
Effective search space:   398682
Effective search space used:   398682
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
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