GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Shewanella amazonensis SB2B

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 6939098 Sama_3196 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__SB2B:6939098
          Length = 454

 Score =  375 bits (964), Expect = e-108
 Identities = 202/446 (45%), Positives = 276/446 (61%), Gaps = 6/446 (1%)

Query: 2   FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYL 61
           F +VLVANRGEIAVR++RAC +LG+ TVA+YS ADK   H   A     IGPA A DSYL
Sbjct: 7   FKRVLVANRGEIAVRIIRACHQLGLETVAIYSSADKGALHTLLATHCLCIGPAAAKDSYL 66

Query: 62  DHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARS 121
           +  +++EAA+   ADAIHPGYGFLAE A FAR V ++   ++GP AD +  +G+K  A  
Sbjct: 67  NINAILEAAKLTAADAIHPGYGFLAERAGFARAVTEAGLVFLGPDADTIATMGDKVSAIK 126

Query: 122 LMQDADVPVVPGTTEPA-DSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
            ++   +P +PG+     D    V+A+A D GYPV IKA  GGGGRG++ V S DE+   
Sbjct: 127 SIKAVGIPTLPGSDGALNDDMNAVEALATDIGYPVLIKASAGGGGRGMRRVDSADELASA 186

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
               + E  A F + +VY+EK+L  PRHIE Q+LAD    +  LGERDCS QRRHQK+IE
Sbjct: 187 IALTRSEALAAFGDNTVYLEKFLTHPRHIEFQMLADGEAAL-CLGERDCSAQRRHQKLIE 245

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300
           EAP+  ++ +    + +      R   Y   GT EFL +DG F+F+E+NTRIQVEHTVTE
Sbjct: 246 EAPALGIAREKIREMADICEAACRRLGYRGVGTFEFLYQDGAFFFIEMNTRIQVEHTVTE 305

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
            VTGLD++ WQL+VA G  L       +++GH++E RINAEAP+ +  P+ G ++    P
Sbjct: 306 MVTGLDLIAWQLKVALGHPL---PPRPQVQGHAIECRINAEAPQSQL-PSPGVITQLRVP 361

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG G+R D  +  G  +   YDS+I KLI  G  REE   R  +AL E +I+G+      
Sbjct: 362 GGPGVRWDSYLFPGAMVPAFYDSLIGKLICHGVTREEATARLRQALTELEIQGIAINKSL 421

Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDP 446
           H  ++  +AF+       ++D +  P
Sbjct: 422 HLQLIACDAFQPWQRDIHFVDALSAP 447


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: 567
Number of extensions: 24
Number of successful extensions: 5
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: 601
Length of database: 454
Length adjustment: 35
Effective length of query: 566
Effective length of database: 419
Effective search space:   237154
Effective search space used:   237154
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: 52 (24.6 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