GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malF_Aa in Pseudomonas fluorescens FW300-N2E3

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate AO353_25120 AO353_25120 ABC transporter permease

Query= uniprot:C8WUR0
         (321 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25120
          Length = 320

 Score =  139 bits (349), Expect = 1e-37
 Identities = 97/312 (31%), Positives = 163/312 (52%), Gaps = 39/312 (12%)

Query: 14  ERAKRRVDWVAYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQFVGLKNYEEL 73
           +R + R  W+   +L+P L+ + +++  P+  T + S T+ N        FVGL NY  L
Sbjct: 22  QRRRVRAAWL---FLTPMLLCLALVAAWPLLRTFWFSLTDANLADTSGGSFVGLSNY--L 76

Query: 74  LNPHDPLSNLFLPTFIW-----TLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLL 128
            +     S + +    W     TL + + +  L  ++GL +A+LLN K    R+L R L+
Sbjct: 77  FHDGSNWSGILVDPQWWNAVRNTLHFTVVSVGLEIVLGLLVALLLNIK-FTGRSLVRALI 135

Query: 129 IVPWAVPNLISMLAWQGLLNDQYGQINALLH--GVFGLPRIPWLTSALWARIAVIMVNVW 186
           ++PWA+P ++S   W  +LNDQ+G IN L+   G+   P + W   A  +  AVI+V+VW
Sbjct: 136 LIPWAIPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAP-LAWTADADLSMWAVIIVDVW 194

Query: 187 AGFPYMMTVCLGALQSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSY-- 244
              P++  + L ALQ +P+D YEAA +DG +  +VF        WR++LPLL+P+     
Sbjct: 195 KTVPFVTLLMLAALQMLPSDCYEAARVDGIHPLKVF--------WRVTLPLLMPALLVAA 246

Query: 245 ------NFNNFNASYLLTGGGPPNSNNPFLGQTDILATAAYKMTLTFNRYDLGATISVLL 298
                 +   F+  Y+LT     NS++     T  ++  A +  + F     G+  S LL
Sbjct: 247 IFRILDSLRVFDVIYVLTS----NSSS-----TMSMSVYARQHLVEFQDVGYGSAASTLL 297

Query: 299 FILVALISWVQM 310
           F++VA+I+ + +
Sbjct: 298 FLVVAVIAMLYL 309


Lambda     K      H
   0.327    0.140    0.451 

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: 318
Number of extensions: 16
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: 321
Length of database: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
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: 48 (23.1 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