GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Pantoea rwandensis LMG 26275

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_084931850.1 HA51_RS03335 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_002095475.1:WP_084931850.1
          Length = 360

 Score =  317 bits (811), Expect = 4e-91
 Identities = 177/368 (48%), Positives = 229/368 (62%), Gaps = 16/368 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA V L  + KRYG   V+H +DL + D  F  LVGPSGCGKST LR++AGLE +S G I
Sbjct: 1   MASVELVNVAKRYGKQSVLHPLDLTIPDGSFTVLVGPSGCGKSTLLRLLAGLESLSDGTI 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
            +   K+ND  P  R+I+MVFQSYALYPH+TVAEN+ F +++     EE ++++   A I
Sbjct: 61  MMDKVKINDRDPADRDIAMVFQSYALYPHLTVAENLAFHMQVKKVKREEQQSKIERIAGI 120

Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180
           L +  LL+R P  LSGGQRQRVAMGRA+VR P VFLFDEPLSNLDA+LR ++R EIK LH
Sbjct: 121 LGIDKLLQRYPRALSGGQRQRVAMGRAMVRNPQVFLFDEPLSNLDAQLRMELRAEIKSLH 180

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
            R + TM+YVTHDQVEAMTL+D+IV+MR+G I Q G P  ++ RPA  FVA FIGSPPMN
Sbjct: 181 QRFKTTMVYVTHDQVEAMTLADQIVVMREGRIVQQGAPLAIYDRPADTFVARFIGSPPMN 240

Query: 241 MEEAVLTDGK---LAFASGATLPLPPRFRSL--VREGQKVTFGLRPDDVYPSGHGLHAGD 295
           +  A L   +            PLPPR++++   REG  VT G RP D+  +     A  
Sbjct: 241 LLPAQLISREGIPGVQCHDLWQPLPPRWQTVGREREGDNVTLGARPHDLIETESRALAS- 299

Query: 296 ADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLF 355
                     V + E  G  TL+   ++G     ++        G+ + + F+  R HLF
Sbjct: 300 ----------VKVVEITGESTLLHLDWHGHALHMQVAGRHHAVSGDEMRIGFNAERIHLF 349

Query: 356 DGETGRAL 363
           D ETG  L
Sbjct: 350 DAETGLRL 357


Lambda     K      H
   0.320    0.137    0.397 

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: 401
Number of extensions: 22
Number of successful extensions: 4
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: 365
Length of database: 360
Length adjustment: 29
Effective length of query: 336
Effective length of database: 331
Effective search space:   111216
Effective search space used:   111216
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 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