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, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate 5210426 Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__PV4:5210426
          Length = 1094

 Score =  321 bits (823), Expect = 9e-92
 Identities = 203/611 (33%), Positives = 324/611 (53%), Gaps = 67/611 (10%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           +F+++L+ANRGEIA+R+ + C ++G+ ++A+Y+E D    H + AD+A  +   R   +Y
Sbjct: 4   VFNRILIANRGEIAIRIAQTCADMGIDSLAIYAEDDSQSLHTKKADQAVAL-KGRGVKAY 62

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           LD E +I  A+    DA+HPGYGFL+EN+ F+++  +    ++G SA+ ++ LG K  AR
Sbjct: 63  LDIEQLIAVAKAHGCDAVHPGYGFLSENSSFSKRCHEEGICFIGSSAELLDLLGNKATAR 122

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYG--YPVAIKAEGGGGGRGLKVVHSEDEVD 178
                +D P+  G  +P  S E+V+A     G    V IKA  GGGGRG++ V   +++ 
Sbjct: 123 ETALRSDTPLTGGINKPC-SLEEVQAFFTSLGDGAAVMIKALAGGGGRGMRPVSRYEDLA 181

Query: 179 GQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKV 238
             +   + E    F +  +YVE+ ++  RHIEVQIL D  G   H  ER+C+LQRR+QK+
Sbjct: 182 EAYRQCREEAIIAFGSGELYVEQLVQHARHIEVQILGDGTGAAVHAWERECTLQRRNQKL 241

Query: 239 IEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV---EDGEFYFMEVNTRIQVE 295
           +E APSP+L +  R  I E+A +     +Y   GT EFL+   +  +FYFME+N RIQVE
Sbjct: 242 LEIAPSPSLDDATRMPIIESALQLASDVKYQGLGTFEFLLDADDHSKFYFMEINPRIQVE 301

Query: 296 HTVTEEVTGLDVVKWQLRVAAGEEL-DFSQDDVEIE-GHSMEFRINAE--APEKEFAPAT 351
           HT+TEE+TGL++VK Q+ + AG+ L + S  +  I+ G +++ RIN E   P+    PA+
Sbjct: 302 HTITEEITGLNLVKLQILLGAGKTLAELSLTEAPIKRGCAIQARINLEQMLPDGSTKPAS 361

Query: 352 GTLSTYDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDI 411
           G +  Y  P G  +R+DD +  G ++   YDS+ AK+I  G D    L +   +L   +I
Sbjct: 362 GVIKAYQVPNGHNVRVDDYLYAGYKVSPSYDSLGAKIIAKGEDFSAALNKVYLSLKALNI 421

Query: 412 EGLRTVIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVT 471
           +G+++       +L  E  +    +T++             VE    E +A D+      
Sbjct: 422 DGVQSNKALLMNLLQREEVQHNRLSTRF-------------VEAHMAELLADDDHH---- 464

Query: 472 ERTFTVEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQQVIEGD 531
           E  F +  + +      E   A  IP G                                
Sbjct: 465 EHFFNIASDQQ------ETVQAVNIPAG-------------------------------- 486

Query: 532 GESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGE-GDS 590
            E V +   G ++ V ++ GD+V  G  + ++EAMKME  V +E  G V++VL G  G+ 
Sbjct: 487 CEGVKSPTAGVLVQVNIESGDEVFAGQEIAVIEAMKMEIPVKSEHAGIVTEVLTGNIGEV 546

Query: 591 VDMGDVLLVLE 601
           +D   +L V++
Sbjct: 547 IDEHQILAVIQ 557


Lambda     K      H
   0.312    0.132    0.371 

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: 1361
Number of extensions: 80
Number of successful extensions: 6
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: 601
Length of database: 1094
Length adjustment: 41
Effective length of query: 560
Effective length of database: 1053
Effective search space:   589680
Effective search space used:   589680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 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