GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Pseudomonas stutzeri RCH2

Align Monocarboxylic acid transporter (characterized)
to candidate GFF346 Psest_0347 probable sodium:solute symporter, VC_2705 subfamily

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__psRCH2:GFF346
          Length = 589

 Score =  146 bits (369), Expect = 2e-39
 Identities = 87/293 (29%), Positives = 145/293 (49%), Gaps = 5/293 (1%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I++  V     + + + V      + +FY  G       NG+A A D++SAASF+ + G 
Sbjct: 6   INMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAGL 65

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           I+  GY   +Y +G+   +++  +L+A  LR  G+FT+ D +  R   +  R+ A    +
Sbjct: 66  IASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVVCLI 125

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            +++ Y+I QMAGAG   S  L++      +  + I   ++ AY + GGMKG TY Q+ +
Sbjct: 126 LISVTYVIGQMAGAGVAFSRFLEVS----NSAGIWIAAAIVFAYAVFGGMKGITYTQVAQ 181

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
            ++L+    I  V   ++++G    +       H  S        D          Y A 
Sbjct: 182 YIVLIIAYTIPAVFIAMQLTGNPIPMFG-MFGTHVDSGVPLLDKLDQVVTDLGFAAYTAD 240

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYL 315
           +  +L+     L+L +GTAGLPHV++RF+TVP   +AR S  W +V I   YL
Sbjct: 241 VDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYL 293



 Score = 72.0 bits (175), Expect = 6e-17
 Identities = 61/201 (30%), Positives = 100/201 (49%), Gaps = 12/201 (5%)

Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416
           + LI+A A A  L+  AGL +  S+A+ HD+   +I N + +E  ++  +R+++    L+
Sbjct: 395 IGLIAAGAIAAALSTAAGLLLAISSAISHDLIKTLI-NPKISEKNEMLAARLSMTAAILL 453

Query: 417 SIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLL 476
           +  LG L      A +VALAF +AA++  P ++  ++ K+ N+ GAVA +  G+IS  + 
Sbjct: 454 ATWLG-LNPPGFAAQVVALAFGLAAASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVY 512

Query: 477 IFLSPA---VSGNDS-AMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLV--GKPDNMDD 530
           IFL      + G  S    P   W     +  G V   L F   +  ++     P  + D
Sbjct: 513 IFLYLGWFFIPGTASIPNTPDQWWMGISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQD 572

Query: 531 LAAEMEVRSLTGVGVEKAVDH 551
           L     VR+  G GV  A+DH
Sbjct: 573 LVE--SVRTPKGAGV--ALDH 589


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: 640
Number of extensions: 29
Number of successful extensions: 4
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: 589
Length adjustment: 36
Effective length of query: 515
Effective length of database: 553
Effective search space:   284795
Effective search space used:   284795
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 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:

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