Alignments for a candidate for pccA in Phaeacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Phaeacidiphilus oryzae TH49

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_051940515.1 BS73_RS25280 biotin carboxylase N-terminal domain-containing protein

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



>NCBI__GCF_000744815.1:WP_051940515.1
          Length = 718

 Score =  441 bits (1134), Expect = e-128
 Identities = 285/731 (38%), Positives = 398/731 (54%), Gaps = 87/731 (11%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MF+ +L+ANRGEIA RVI+T R++GI++V +++  D +A HVR AD AV IG       Y
Sbjct: 1   MFETVLVANRGEIARRVIRTLRRLGIRSVVVHTRPDADAPHVRDADTAVEIG------GY 54

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           + I  ++DA  +TGAEAVHPGYGFL+EN  FA A    G+ FIGPPA AIE MGDKI +K
Sbjct: 55  LDIQAILDAAARTGAEAVHPGYGFLAENAGFARACAAAGLVFIGPPAEAIELMGDKIHAK 114

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
               EA V  VPG  G     D+    + +IG PV++K SAGGGGKGMR+  +++   E 
Sbjct: 115 AAVSEAGVPVVPGSEGDRLTDDQLAAAARDIGMPVLLKPSAGGGGKGMRLVRDESALAEE 174

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
             +++ EA  SFG+D + +E+++ +PRHIEIQVLAD HG  ++LGERECS+QRR+QK++E
Sbjct: 175 IAAARREARASFGNDTLLVERWIDRPRHIEIQVLADAHGRIVHLGERECSLQRRHQKLIE 234

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVD--GDRNFYFLEMNTRLQVEHP 298
           EAPS  LD  TR AMG+ +   A A GY  AGTVEFIV      ++ F+EMNTRLQVEHP
Sbjct: 235 EAPSALLDPETRAAMGQAAVRAAAACGYTGAGTVEFIVPTADPSSYSFMEMNTRLQVEHP 294

Query: 299 VTELI------------TGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYR 346
           VTEL             T +DLVEQ +RVAAGE L  TQ D + +G A+E R+ AEDP R
Sbjct: 295 VTELAASIDGLPGASGPTSLDLVEQQLRVAAGEPLAFTQSDFSFSGHAVEARICAEDPAR 354

Query: 347 NFLPSIGRLTRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMI 406
           +FLP+ G +     P    +GPL+  G            VR D+G+  G E+   YDPM+
Sbjct: 355 DFLPTGGTVLLLDEP----SGPLDRTG------------VRVDSGLAAGTEVGSSYDPML 398

Query: 407 AKLCTWGPDRPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYP 466
           AK+   GPDR +A+  +R AL G  + G+  N  ++  ++ HP    G++ T  + E++P
Sbjct: 399 AKVIARGPDRESALRLLRGALAGTRILGVTTNAGYLRRLLHHPEVRSGDLDTGLV-ERHP 457

Query: 467 DGFEGVTLGAADLTRLAAAAAAMFRVAEIRRTR--ISGTLDNHERMVGTDWVVTAQDA-- 522
           +    +T+  A  TR A + AA+ R   +       +G  D   R  G  W + A+ A  
Sbjct: 458 E----LTVPPAADTRDALSVAALVRQLTLAPAADPRTGWQDPFARPSG--WRLGAEPAWT 511

Query: 523 --RFDVTIDADPGGSTVRFADGTAHRVT-----SRWTPGDSLATVEID------------ 563
             R       D GG  V      A   T        T   S+ T E+             
Sbjct: 512 RHRLVPRSGPDAGGEPVEIRIRPASATTLTDAADNATDQGSVHTFEVRHGENPPVVVRLC 571

Query: 564 -------GAPMVLKVDKITSGFR----------MRFRGADVKVHVRTPRQAELNDLMPEK 606
                  G  +++ +D +T+ +           +  RG         P    L +L    
Sbjct: 572 QDADNAVGRRLLITLDGLTTAWTTATAPDGTVWLSARGETWSFAPHDP----LAELALAG 627

Query: 607 LPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATVTKINAG 666
                   L  PMPG V  + V  GD V +GQ L  +EAMKME+++ A     V ++ A 
Sbjct: 628 PAAAHGGALNAPMPGTVTLVKVAEGDRVTQGQPLLVLEAMKMEHVIAAPHDGLVERLKAR 687

Query: 667 AGDSLAVDDVI 677
            G ++A+D+++
Sbjct: 688 PGATVAMDELL 698


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: 1259
Number of extensions: 70
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 681
Length of database: 718
Length adjustment: 39
Effective length of query: 642
Effective length of database: 679
Effective search space:   435918
Effective search space used:   435918
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 Apr 09 2024. 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)
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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