GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Porphyrobacter dokdonensis DSW-74

Align Monocarboxylic acid transporter (characterized)
to candidate WP_068865628.1 I603_RS12870 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_001677335.1:WP_068865628.1
          Length = 591

 Score =  153 bits (387), Expect = 2e-41
 Identities = 100/308 (32%), Positives = 158/308 (51%), Gaps = 26/308 (8%)

Query: 27  VVFIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           ++++ V  +  L +G         +++FY  G   +   NG+A A D++SAASF+ + G 
Sbjct: 6   LIYLFVGASFALYIGIAIWSRAGSTSEFYVAGGGVNPVVNGMATAADWMSAASFISMAGI 65

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           I+  GYD  +Y +G+   +++  LL+A  LR  G+FT+ D +  R   K  RV A    +
Sbjct: 66  IAFTGYDASVYLMGWTGGYVLLALLLAPYLRKFGQFTVPDFIGTRYYSKAARVVAVICLI 125

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V+  Y+  QM G G + S  LD+       VV+G +GIV + Y +LGGMKG TY Q+ +
Sbjct: 126 LVSFTYIAGQMRGVGIVFSRFLDVD--ITTGVVIG-MGIVFV-YSVLGGMKGITYTQVAQ 181

Query: 203 AVLLVGGVAIMTVLTFVKVSG------GLTTLLNDAVEKHAASDYAATKGYDPTQILEPG 256
             +L+    +        ++G      GL + + D     A+  Y   K      ++  G
Sbjct: 182 FCVLIFAYMVPAFFLSFMITGNPVPQFGLGSKVGD-----ASGLYVLQK----LDLVLTG 232

Query: 257 LQYGATLTTQ---LDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAF 313
           L + A    Q   +D   + LAL +GTAGLPHV++RF+TVP A +AR S  WA++ I   
Sbjct: 233 LGFAAYTAGQKSMIDVFCITLALMVGTAGLPHVIVRFFTVPKASDARLSAGWALIFIALL 292

Query: 314 YLMTLVLG 321
           Y     +G
Sbjct: 293 YTTAPAVG 300



 Score = 63.9 bits (154), Expect = 2e-14
 Identities = 50/158 (31%), Positives = 75/158 (47%), Gaps = 10/158 (6%)

Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416
           +AL++A   A  L+  AGL +  SAAV HD+     R   S + E +         IG  
Sbjct: 403 IALVAAGGLAAALSTAAGLLLVISAAVSHDLLKQTFRPAISEKGELLAARLAATAAIG-- 460

Query: 417 SIVLGILAMTQN--VAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISAL 474
             V G L +     VA +VA AF +AA++  P IL  ++ K+ N  GA+A + +GL    
Sbjct: 461 --VAGYLGINPPGWVAQVVAFAFGLAAASLFPAILMGIFSKRMNREGAIAGMVSGLAFTF 518

Query: 475 LLIFLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLA 512
             I     VS + S     A+W +F +   G+  I +A
Sbjct: 519 GYIVWFKLVSPDTST---AANW-LFGISPEGIGVIGMA 552


Lambda     K      H
   0.324    0.138    0.393 

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: 674
Number of extensions: 42
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 591
Length adjustment: 36
Effective length of query: 515
Effective length of database: 555
Effective search space:   285825
Effective search space used:   285825
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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