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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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:

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:

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:

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:

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