GapMind for catabolism of small carbon sources

 

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

Align Proline-specific permease (ProY) (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= TCDB::P37460
         (456 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  528 bits (1360), Expect = e-154
 Identities = 250/441 (56%), Positives = 335/441 (75%), Gaps = 1/441 (0%)

Query: 7   LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66
           LKR L  RHIR MALG+ IG GLF GSA AI+MAGP+++L+YIIGG+A  +IMRALGEM+
Sbjct: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77

Query: 67  VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126
           VHNP A SFSRYAQ+ LGPLAG++TGW Y F  L+  +A++TA  +YMG+WFP VP WIW
Sbjct: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137

Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186
            L+ ++ + +INL++VK FGE EFWF+  K+ TII M++ G+GII +G GN G   GI N
Sbjct: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197

Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246
           LW++GGF  NG  G++MSLQMVMFAY G+E+IG+TAGEAK+P+K+IP AI SV  RIL+F
Sbjct: 198 LWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257

Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306
           YVG LFVI+SIYPWN++GT GSPFV+TF+ +GI  AA I+NFVV+TA+LS+ N  +F  G
Sbjct: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317

Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLATF 366
           RML+ +A+ G AP  FA TS  G+P   +L+   ALL  V LNY++PE VF+ + S+ATF
Sbjct: 318 RMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377

Query: 367 ATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPDTR 426
             +W W+MILL+Q+ FR+ L   E  ALK+++    V++   L FLV ++ L+ Y PDTR
Sbjct: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437

Query: 427 ISLYVGFAWIVLL-LIGWIFK 446
           ++LYVG A++VLL ++ ++FK
Sbjct: 438 VALYVGPAFLVLLTVLFYVFK 458


Lambda     K      H
   0.329    0.143    0.449 

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: 729
Number of extensions: 37
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: 456
Length of database: 473
Length adjustment: 33
Effective length of query: 423
Effective length of database: 440
Effective search space:   186120
Effective search space used:   186120
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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