GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Pseudomonas fluorescens FW300-N2C3

Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate AO356_28575 AO356_28575 ABC transporter permease

Query= TCDB::O30832
         (290 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28575
          Length = 320

 Score =  128 bits (321), Expect = 2e-34
 Identities = 95/295 (32%), Positives = 155/295 (52%), Gaps = 19/295 (6%)

Query: 9   AARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYY--------FL 60
           AA L ++P ++ L L    PL  T +FS    +L   G  +F G  NY +         L
Sbjct: 28  AAWLFLTPMLLCLALVAAWPLLRTFWFSLTDASLADTGDATFVGLSNYLFHSSAGWSGLL 87

Query: 61  TDPAFSAALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSA 120
            DP +  A+ NT+   V  + + +V G+L+ALLL+  F G+ +VR L++ P+ +   VSA
Sbjct: 88  VDPQWWNAVRNTLHFTVVSVGLEIVLGLLVALLLNVRFSGRALVRALILIPWAIPTIVSA 147

Query: 121 LVWKNMFMNPVNGMFAHIARGLGL--PPFDFLSQAPLA--SIIGIVAWQWLPFATLILLT 176
            +W  M +N   G+  H+  GLGL   P  + + A L+  ++I +  W+ +PF TL++L 
Sbjct: 148 KIWSWM-LNDQFGIINHLMLGLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFVTLLMLA 206

Query: 177 ALQSLDREQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNG 236
           ALQ L  +  EAA +DG   +  F  +T+P L  A+ V  + + +  L VF  I V T+ 
Sbjct: 207 ALQMLPSDCYEAARVDGIHPVKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVIYVLTSN 266

Query: 237 GPGTASTNITYLVYA-QSLLNY-DVGGGSAGGIVAVVLANIVAIFLMRMIGKNLD 289
              T S +    VYA Q L+ + DVG GSA   +  ++  ++A+  + +  + L+
Sbjct: 267 SSSTMSMS----VYARQHLVEFQDVGYGSAASTLLFLVVAVIAMVYLYLGRRQLE 317


Lambda     K      H
   0.329    0.142    0.429 

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: 213
Number of extensions: 9
Number of successful extensions: 4
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: 290
Length of database: 320
Length adjustment: 27
Effective length of query: 263
Effective length of database: 293
Effective search space:    77059
Effective search space used:    77059
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 (21.8 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