GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Sinorhizobium meliloti 1021

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate SMa2207 SMa2207 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Smeli:SMa2207
          Length = 361

 Score =  206 bits (525), Expect = 6e-58
 Identities = 140/361 (38%), Positives = 207/361 (57%), Gaps = 27/361 (7%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I V+ ++K +  G + A+DNV+ ++  GE   +LGPSG GKTT +R+IAG   PS G L 
Sbjct: 6   IQVEGITKRY--GAMTAVDNVSFDVGQGEFVSLLGPSGCGKTTTLRMIAGFVDPSGGLLR 63

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123
              R V       +PPE R +G VFQ +AL+P++T  EN+AF L   K ++  IR +V E
Sbjct: 64  VRGRDVTH-----LPPEKRDLGFVFQNYALWPHMTVAENVAFGLKLRKKNRNFIRDKVAE 118

Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183
                 +    N  PR+LSGGQQQRVALARAL  +P +LL+DEP SNLD  +R + R  +
Sbjct: 119 ALTTTGLSGYENRLPRQLSGGQQQRVALARALALEPQVLLMDEPLSNLDRALRVTMRREL 178

Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243
           KE+Q+R+ +T L V+HD  +  ++++RV ++ KG++ QV  P +LY+NP +  VA  +G 
Sbjct: 179 KELQARMKMTTLYVTHDQEEALSMSNRVVIMNKGQVEQVAAPFELYENPATGFVADFVGI 238

Query: 244 INELEGKVTN-EG----VVIGSLRFPVSVSSDRAIIG------IRPEDVKLSKDVIKDDS 292
            N L G VT+ EG    V +GS +   +V+     +G      IRPE V L       D+
Sbjct: 239 TNFLGGIVTSAEGGGVEVKLGSGQMLRAVTKQPVALGTKVRALIRPERVTLKTTAADGDN 298

Query: 293 WILVGKGKVKVIGYQGGLFRITITPLDSEE----EIFTYSDHPIHSGEEVLVYVRKDKIK 348
              +  G+V +  Y G L R ++  LDS +    E+  + D  I SG  V V V  + ++
Sbjct: 299 ---ILTGQVVLAEYFGALLRYSVR-LDSGDILRAEVHNF-DSFIESGSRVWVCVSPEHLR 353

Query: 349 V 349
           +
Sbjct: 354 L 354


Lambda     K      H
   0.319    0.139    0.390 

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: 293
Number of extensions: 12
Number of successful extensions: 2
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: 353
Length of database: 361
Length adjustment: 29
Effective length of query: 324
Effective length of database: 332
Effective search space:   107568
Effective search space used:   107568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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