GapMind for catabolism of small carbon sources

 

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

Align L-alanine and D-alanine permease (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



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

 Score =  711 bits (1834), Expect = 0.0
 Identities = 338/442 (76%), Positives = 394/442 (89%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           L+R L ERHIRLMALG+ IGVGLFLGSA AI +AGPAI+LSY++GG+AI +IMRALGEMA
Sbjct: 7   LQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGEMA 66

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137
           V NPVAGSFSRYAQDYLGPL G+LTGWNYWF+WL+TC+AEITAV VYMG+WFPDVP+WIW
Sbjct: 67  VQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQWIW 126

Query: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197
           ALAALV+MG++NL AVKA+GEFEFWFA+IK+VTI+ M++GG  +I FG GN GV  GISN
Sbjct: 127 ALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPTGISN 186

Query: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257
           LW HGGFMPNG  G+LM+LQMVMFAYLGVEMIGLTAGEA NP+K+IP+AI SVFWRIL+F
Sbjct: 187 LWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRILIF 246

Query: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317
           YVGALFVI+SIYPWNE+GT GSPFVMTFERLGIK+AAGIINFVV+TAALSSCNGGI+STG
Sbjct: 247 YVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGIYSTG 306

Query: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377
           RML++LAQ GQAP  FA TS +G+P RA+L+S+ ALL GVLLNYLVP KVFVWVTS ATF
Sbjct: 307 RMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVTSAATF 366

Query: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437
           GAIWTW ++L+ Q+K+R+ LS ++R+ L +RM  +P +SYLALAFLVLVVGLM YFPDTR
Sbjct: 367 GAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGYFPDTR 426

Query: 438 VALYVGPAFLVLLTVLFYTFKL 459
           VAL VGP +LVLLTVL+Y F L
Sbjct: 427 VALIVGPLWLVLLTVLYYVFGL 448


Lambda     K      H
   0.328    0.142    0.444 

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: 821
Number of extensions: 34
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: 473
Length of database: 454
Length adjustment: 33
Effective length of query: 440
Effective length of database: 421
Effective search space:   185240
Effective search space used:   185240
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: 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