GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3211
          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:

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