GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Sinorhizobium meliloti 1021

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate SM_b20002 SM_b20002 sugar ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Smeli:SM_b20002
          Length = 358

 Score =  360 bits (925), Expect = e-104
 Identities = 199/359 (55%), Positives = 250/359 (69%), Gaps = 26/359 (7%)

Query: 17  VGSLQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSV 76
           +  LQL  +RK++G  EV+KG+DLD+K GEFV+FVGPSGCGKSTLLR IAGLE+ +SG +
Sbjct: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60

Query: 77  QIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGM 136
            ID V +  V P+KRGIAMVFQSYALYPH+TV++NMG  L+ AGVP+AEIE++V +AA +
Sbjct: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120

Query: 137 LSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLH 196
           L L   L R+P +LSGGQRQRVAIGRAIVR PK+FLFDEPLSNLDA LRV+ R+EIARLH
Sbjct: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180

Query: 197 RSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMN 256
           + L  T++YVTHDQVEAMTLADKIVV+ AG +EQVGSP++LY+ PANLFVAGFIGSP+MN
Sbjct: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240

Query: 257 FIEA----------AKLGD--------------GEAKTIGIRPEHIGLSRESGDWKGKVI 292
           F++           A+L D              G A TIGIRPEH   +  +      + 
Sbjct: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFDEAGPAA-LDLAID 299

Query: 293 HVEHLGADTIIYIESETVG-LLTVRLFGEHRYATDDIVHATPVIGSMHRFDADGRVIKS 350
            +EHLG +T  Y      G L+ V         T D + A     S+  FD +G+ ++S
Sbjct: 300 MLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLRS 358


Lambda     K      H
   0.320    0.137    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: 394
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: 352
Length of database: 358
Length adjustment: 29
Effective length of query: 323
Effective length of database: 329
Effective search space:   106267
Effective search space used:   106267
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 (21.8 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