GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Sinorhizobium fredii NGR234

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

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



>NCBI__GCF_000018545.1:WP_164924745.1
          Length = 355

 Score =  351 bits (900), Expect = e-101
 Identities = 188/367 (51%), Positives = 249/367 (67%), Gaps = 16/367 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           M  VT++ + KRYGAL V+  +   ++D EF+ LVGPSGCGKST LRM+AGLEE+SGG +
Sbjct: 1   MTDVTIRNVTKRYGALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGGDL 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
            +G   +ND P + R++++VFQ+YALYPHMTVAENMGF+LK+  RP  EI  RV +AAAI
Sbjct: 61  LMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAAAI 120

Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180
           L L  LL+R P  LSGGQRQRVAMGRAIVR P VFLFDEPLSNLDAKLR Q+R EIK LH
Sbjct: 121 LGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKALH 180

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
            R++ T +YVTHDQ+EAMT++D+IV+M +G +EQ+GTP +++ RPA  FVAGFIGSP MN
Sbjct: 181 QRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPSMN 240

Query: 241 MEEAVL--TDGK-LAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDAD 297
              A +  T+G  L    G  LP+       +    +VT+G+RP+ +     G+ A    
Sbjct: 241 FLPATVAATNGPLLKTPEGVALPIDG--GPTLTGRSEVTYGIRPEHLQLGETGIPA---- 294

Query: 298 AVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDG 357
                   V + EP G+ET ++    GR+ V+ + +   +RPGE + ++     AHLFD 
Sbjct: 295 -------EVVVVEPTGSETQLYVTVGGREVVAVLRDRVDVRPGEKIWLTPRKGCAHLFDP 347

Query: 358 ETGRALA 364
            TG  +A
Sbjct: 348 NTGARIA 354


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: 414
Number of extensions: 17
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: 365
Length of database: 355
Length adjustment: 29
Effective length of query: 336
Effective length of database: 326
Effective search space:   109536
Effective search space used:   109536
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 Apr 09 2024. 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