GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Sinorhizobium meliloti 1021

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Smeli:SM_b21344
          Length = 497

 Score =  300 bits (769), Expect = 6e-86
 Identities = 176/474 (37%), Positives = 268/474 (56%), Gaps = 5/474 (1%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           + K F    AL   S+ V   E  ALVG+NGAGKSTL+ ILTG  + D G V F+G    
Sbjct: 8   ICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVFAGEGVS 67

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWK 139
                ++    +A +YQ   +    SVAEN++++R+P R G+ID +AMR  A A+L  + 
Sbjct: 68  FSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAAAVLRAFN 127

Query: 140 IDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQRE 199
           +++  D      S   RQ+V IARA++  AR +I+DEPT+ LD  E+  LF  I  L+R 
Sbjct: 128 LEIDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDTIRTLKRG 187

Query: 200 GVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADAA 259
           GV+ +FI H L+E+Y IC  VT++RD + + +A ++ +P+  L+  M G+   LA  +A 
Sbjct: 188 GVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKE--LAAFEAI 245

Query: 260 ARGA-LPADTAVALELKEL-TGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317
           A+ A   A   V L ++    G     VS TV+ GE+ GL G   SGRT  A  I G   
Sbjct: 246 AKDADEGAQRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTETANLIFGADR 305

Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377
            +RG I  +G          ++A GIG V +DR  +G++   S+ EN ++ +   L + G
Sbjct: 306 LQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLALLPKLARAG 365

Query: 378 IAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTA 437
           I   A+++   ++ I AL I    P+  +  LSGGNQQKV++ R L T+P +L++ +PT 
Sbjct: 366 IVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLLIVDEPTR 425

Query: 438 GVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEFP 490
           G+D+ +K  +L ++ R+ +EG  VL++S EL++ L   DRV V+  G   A  P
Sbjct: 426 GIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSVAVLP 479



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 69/230 (30%), Positives = 108/230 (46%), Gaps = 17/230 (7%)

Query: 25  GSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADR 84
           G+   + DVS+ V  GE   L G  G+G++   +++ G  +   GE+R++G A       
Sbjct: 265 GAGVRVRDVSLTVREGEISGLAGLLGSGRTETANLIFGADRLQRGEIRYNGEARAYRQPA 324

Query: 85  DAWRERVACVYQHST---IIRDLSVAENLFINRQP--LRGGVIDWQAMRRDARALLDHWK 139
           DA  + +  V +      II D+S+ EN+ +   P   R G++D           +    
Sbjct: 325 DAIADGIGLVAEDRKVDGIIPDMSIRENMTLALLPKLARAGIVDRARQDEIVERYITALA 384

Query: 140 IDVRE-DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLD---GDEIKRLFRRISE 195
           I     D    +LS   +Q V + R L    + +I+DEPT  +D     EI RL RR+++
Sbjct: 385 IKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLLIVDEPTRGIDIGAKSEILRLLRRLAD 444

Query: 196 LQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEA 245
              EG+  L IS  L+E+      VTVL D        V+ LPR++L EA
Sbjct: 445 ---EGLGVLMISSELEELLAAADRVTVLSD-----GTSVAVLPRKELSEA 486


Lambda     K      H
   0.318    0.134    0.377 

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: 616
Number of extensions: 36
Number of successful extensions: 6
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: 510
Length of database: 497
Length adjustment: 34
Effective length of query: 476
Effective length of database: 463
Effective search space:   220388
Effective search space used:   220388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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