GapMind for catabolism of small carbon sources

 

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

Align lysine-specific permease (characterized)
to candidate PfGW456L13_3211 Arginine permease RocE

Query= CharProtDB::CH_003129
         (489 letters)



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

 Score =  396 bits (1018), Expect = e-115
 Identities = 193/438 (44%), Positives = 287/438 (65%), Gaps = 10/438 (2%)

Query: 13  LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72
           L R LK+RH+ M+++GG IGTGLF+ SG TI+Q GP GA+L+Y++ G ++Y +M  LGEL
Sbjct: 16  LTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGFLMYLVMVCLGEL 75

Query: 73  AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132
           +  MPVSGSF T+   Y+    GF +GW YW +WA T+ ++  AA ++M+ WFP+ P W 
Sbjct: 76  SVQMPVSGSFQTHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIWY 135

Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGI--FKGAQPAGW 190
           WSALF+ V+F +N ++ R FGEAEYWFS IKV  ++ FI+VGVL+I G+       PA  
Sbjct: 136 WSALFVVVLFGINAMATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGVMPLSSGAPAPM 195

Query: 191 SNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRIL 250
           +   IG++ F  G +A+  V M V ++FQG E++G+AAGE++ P K+IPRAVR V +R+L
Sbjct: 196 ATNLIGDSLFPNGLSAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVFRVL 255

Query: 251 LFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLS 310
           +FYV AI+++S I+P+    L+         SPF  VF   G+  AA +MN VILTA+LS
Sbjct: 256 IFYVLAIIVLSAIVPWQQAGLME--------SPFVQVFDMVGIPYAADLMNFVILTAILS 307

Query: 311 AGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQTV 370
            GNSG+YASTR+L+ ++  G AP+  + LS+ GVP  AL  T   A +  +TS     T+
Sbjct: 308 VGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFVAADTL 367

Query: 371 YLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFILCLI 430
           ++ L+  SGM+G + W+ IA++ Y+FR+ Y+  G  + DL YR+ +FP+ P+    LC  
Sbjct: 368 FMVLMAVSGMSGTVTWIVIALAQYKFRKAYLRDGGKLRDLKYRAPWFPVLPLMCITLCCS 427

Query: 431 ITLGQNYEAFLKDTIDWG 448
           + +    +   + ++ WG
Sbjct: 428 LFVFLALDETQRPSLYWG 445


Lambda     K      H
   0.327    0.142    0.451 

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: 786
Number of extensions: 48
Number of successful extensions: 3
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: 489
Length of database: 474
Length adjustment: 34
Effective length of query: 455
Effective length of database: 440
Effective search space:   200200
Effective search space used:   200200
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: 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