GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TAT in Pseudomonas fluorescens GW456-L13

Align tryptophan permease (characterized)
to candidate PfGW456L13_3211 Arginine permease RocE

Query= CharProtDB::CH_091156
         (592 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3211 Arginine
           permease RocE
          Length = 474

 Score =  238 bits (608), Expect = 3e-67
 Identities = 131/400 (32%), Positives = 221/400 (55%), Gaps = 11/400 (2%)

Query: 78  LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137
           L R LK RH+ M+++GG IGTGLF+GSG  I +GGP+G ++ + +AG  +   +  LGE+
Sbjct: 16  LTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGFLMYLVMVCLGEL 75

Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197
           +V+ PV G+F  + T+++ P+  F++  +Y + W   + LE  AA M +  W   +    
Sbjct: 76  SVQMPVSGSFQTHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIWY 135

Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEFIGAKY 257
           W A+F  V+  IN    R FGEAE+ FS IK   + GFI++ V++I G  P      A  
Sbjct: 136 WSALFVVVLFGINAMATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGVMPLSSGAPAPM 195

Query: 258 WHD---PGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQVFWRIL 312
             +        NG   V +V++   Y+  G E+  +A+GETD   K +P A++ V +R+L
Sbjct: 196 ATNLIGDSLFPNGLSAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVFRVL 255

Query: 313 FFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSVG 372
            F+++++ ++  +VP+    L+       SPFV    +  I     ++N VIL ++LSVG
Sbjct: 256 IFYVLAIIVLSAIVPWQQAGLM------ESPFVQVFDMVGIPYAADLMNFVILTAILSVG 309

Query: 373 NSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVFN 432
           NS ++AS+R L +M+  G+ P     + + G PL  +     F L++ +    +   +F 
Sbjct: 310 NSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFVAADTLFM 369

Query: 433 WLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEF 472
            LMA++G++  + W+ I L+  +FR A    G  L +L++
Sbjct: 370 VLMAVSGMSGTVTWIVIALAQYKFRKAYLRDGGKLRDLKY 409


Lambda     K      H
   0.326    0.141    0.447 

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: 777
Number of extensions: 52
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: 592
Length of database: 474
Length adjustment: 35
Effective length of query: 557
Effective length of database: 439
Effective search space:   244523
Effective search space used:   244523
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 (21.6 bits)
S2: 52 (24.6 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