GapMind for catabolism of small carbon sources

 

Aligments for a candidate for potB in Pseudomonas fluorescens FW300-N2E3

Align putrescine transport system permease protein PotH (characterized)
to candidate AO353_29315 AO353_29315 spermidine/putrescine ABC transporter permease

Query= CharProtDB::CH_088338
         (317 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_29315 AO353_29315
           spermidine/putrescine ABC transporter permease
          Length = 304

 Score =  374 bits (961), Expect = e-108
 Identities = 173/286 (60%), Positives = 230/286 (80%)

Query: 28  GRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFL 87
           GRK+VI +P++WL L F+LPF +V KIS +E A AIPPY+E+  +A+ +  + LNLGN+ 
Sbjct: 15  GRKVVIGIPFLWLCLFFMLPFFLVMKISFSEAALAIPPYSEIYSFAEQKFQLLLNLGNYA 74

Query: 88  QLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSF 147
            L DD LY  AYL SL++AA+ST  CL+IG+P+A+A++ +    +N+LLLL+++P+WT+ 
Sbjct: 75  MLGDDELYISAYLGSLKMAALSTAMCLVIGFPMAYAISKASKEAQNVLLLLIMMPTWTAI 134

Query: 148 LIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTAL 207
           LIRVYAWMGIL NNG+LN FLLW G+I +P+ IL+TN AVYIG+VYAY+PFMVLP+Y  L
Sbjct: 135 LIRVYAWMGILSNNGLLNAFLLWTGLISEPIEILNTNTAVYIGVVYAYLPFMVLPLYANL 194

Query: 208 IRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDS 267
           ++ D SL+EAA DLG+     F+ + VPL + GIIAG MLVFIP VGEFVIPELLGGP++
Sbjct: 195 VKHDGSLLEAASDLGSSNFNNFWKITVPLARNGIIAGCMLVFIPVVGEFVIPELLGGPET 254

Query: 268 IMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSV 313
           +MIGRVLWQEFFNNRDWPVASA+A++ML +LIVPI+ F++ Q K +
Sbjct: 255 LMIGRVLWQEFFNNRDWPVASALAVVMLAILIVPIILFNRSQAKEM 300


Lambda     K      H
   0.328    0.144    0.457 

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: 354
Number of extensions: 13
Number of successful extensions: 1
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: 317
Length of database: 304
Length adjustment: 27
Effective length of query: 290
Effective length of database: 277
Effective search space:    80330
Effective search space used:    80330
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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