GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Shewanella oneidensis MR-1

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate 200217 SO1034 iron-compound ABC transporter, permease protein (NCBI ptt file)

Query= SwissProt::P15030
         (332 letters)



>FitnessBrowser__MR1:200217
          Length = 380

 Score =  154 bits (390), Expect = 3e-42
 Identities = 107/311 (34%), Positives = 160/311 (51%), Gaps = 33/311 (10%)

Query: 48  TPTLPEALVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMAL 107
           T  + + +V  LRLPR L+A + GA L+LAG++LQT+T NP+A P L GI+SGA+    +
Sbjct: 72  TAAMTDRIVMELRLPRILLAFVAGAGLSLAGSVLQTVTRNPLADPYLFGISSGASFGAVV 131

Query: 108 TSAL--------------------SPTPIAG---YSLSFIAACGGGVSWLLVMTAGG-GF 143
              L                        +AG   +SL F A  G  +S L+V+   G G 
Sbjct: 132 MLTLFSGSGFFANAGVIANSGIFSGAEILAGLQWFSLPFGAFIGASLSVLIVLALSGLGL 191

Query: 144 RHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHA-YGIFYWLAGGVSHARWQDVWQLLP 202
               +R  ++L+G+A S     LT + L  A   A   + +W  G  + A W  +  +LP
Sbjct: 192 NSQVER--MLLSGVATSFMFGALTSLLLYFASPQATASVLFWSLGSFAKASWSLL--ILP 247

Query: 203 VVVTAVPVVLLLA--NQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPV 260
            +V  V   ++L    Q+  L   D TAHTLGVN+ +LRL + +L  L+    V+  G +
Sbjct: 248 TIVVLVSFFIILGWKRQIMALQAGDETAHTLGVNVPKLRLNMLLLCSLITAILVATCGGI 307

Query: 261 AFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIG 320
            F+GL++PH  R    F  R  + ++ L+G   M+  DVLAR L    +LP G + A IG
Sbjct: 308 GFVGLMIPHTVRLL--FPGRQPILLTALVGGLFMVWIDVLARCLLGNQELPVGIITASIG 365

Query: 321 SPCFVWLVRRR 331
           S  F+ ++RRR
Sbjct: 366 SFFFLLILRRR 376


Lambda     K      H
   0.327    0.140    0.436 

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: 345
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 332
Length of database: 380
Length adjustment: 29
Effective length of query: 303
Effective length of database: 351
Effective search space:   106353
Effective search space used:   106353
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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