GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proY in Dyella japonica UNC79MFTsu3.2

Align Proline-specific permease (ProY) (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= TCDB::P37460
         (456 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2630 N515DRAFT_2630 amino
           acid/polyamine/organocation transporter, APC superfamily
          Length = 454

 Score =  540 bits (1391), Expect = e-158
 Identities = 257/441 (58%), Positives = 337/441 (76%)

Query: 1   MESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMR 60
           M++N+ L+RGL  RHIR MALGSAIG GLF GSA+AI++AGP++LL+Y++GGVA +IIMR
Sbjct: 1   MQTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMR 60

Query: 61  ALGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPA 120
           ALGEM+V NP A SFSRYAQ+ LGPL GY+TGW Y F  L+  IA++TA G+YMGVWFP 
Sbjct: 61  ALGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPD 120

Query: 121 VPHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQ 180
           VP WIW L+ ++ + A+NL +VK +GE EFWF+  KV TI++MIV G  +IV+G+GN G 
Sbjct: 121 VPQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGV 180

Query: 181 PTGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVP 240
           PTGI NLW++GGF  NG  GM+M+LQMVMFAY G+E+IG+TAGEA +P+KSIP AINSV 
Sbjct: 181 PTGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVF 240

Query: 241 MRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINS 300
            RIL+FYVG LFVIMSIYPWN++GT+GSPFV+TF+ +GI  AA I+NFVVLTA+LS+ N 
Sbjct: 241 WRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNG 300

Query: 301 DVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVI 360
            ++  GRML  +A+QG AP+ FA TS  GIP   VLV  +ALLF V LNY++P  VF+ +
Sbjct: 301 GIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWV 360

Query: 361 ASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIG 420
            S ATF  +W W ++L++Q+ +RR L   +   L F++P     +   L FLV ++ L+G
Sbjct: 361 TSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMG 420

Query: 421 YHPDTRISLYVGFAWIVLLLI 441
           Y PDTR++L VG  W+VLL +
Sbjct: 421 YFPDTRVALIVGPLWLVLLTV 441


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: 699
Number of extensions: 32
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: 454
Length adjustment: 33
Effective length of query: 423
Effective length of database: 421
Effective search space:   178083
Effective search space used:   178083
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.

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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 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, 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