GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutW in Pseudomonas fluorescens FW300-N2E2

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Pf6N2E2_3802 Histidine ABC transporter, permease protein (TC 3.A.1)

Query= TCDB::Q9KKE2
         (285 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3802 Histidine ABC
           transporter, permease protein (TC 3.A.1)
          Length = 283

 Score =  352 bits (903), Expect = e-102
 Identities = 179/280 (63%), Positives = 223/280 (79%)

Query: 1   MFPDSLNLSIRAPVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFM 60
           MFP+S   SI   VN ++ ALVTNYG VF+ IS  +L A++ +E +LR  PWWL++    
Sbjct: 1   MFPESFTFSIADWVNGWVDALVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVG 60

Query: 61  ALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKS 120
            +A  ++R+   T  +  LL  VG +G+WD  MQTLALML+AT++SV+IG+P+GIL A+S
Sbjct: 61  GIAWHATRKVVATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARS 120

Query: 121 RVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQV 180
             +R++ +P+LD+MQTMPSFVYLIP LMLFGLGKVPAI AT+IYA PPLIRLTDLGIRQV
Sbjct: 121 NRLRSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQV 180

Query: 181 DAEVVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQ 240
           D EV+EA  AFG +  Q LFGV+LPLA P+IMAG+NQT MMALSMVV+ASMIGARGLGE 
Sbjct: 181 DGEVMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGED 240

Query: 241 VLNGIQTLDVGKGLEAGIGIVILAVVLDRITQGFGKPRTE 280
           VL GIQTL+VG+GLEAG+ IVILAVV+DRITQ +G+PR E
Sbjct: 241 VLVGIQTLNVGRGLEAGLAIVILAVVIDRITQAYGRPRHE 280


Lambda     K      H
   0.327    0.142    0.422 

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: 312
Number of extensions: 14
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: 285
Length of database: 283
Length adjustment: 26
Effective length of query: 259
Effective length of database: 257
Effective search space:    66563
Effective search space used:    66563
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: 47 (22.7 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