GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Herbaspirillum seropedicae SmR1

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS02210
          Length = 372

 Score =  337 bits (864), Expect = 3e-97
 Identities = 182/369 (49%), Positives = 243/369 (65%), Gaps = 16/369 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           MA V+++ L KRY   EV+  I+LE++D EF+  VGPSGCGKST LRMIAGLEE+S G +
Sbjct: 1   MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60

Query: 61  EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120
           +IG R++N++P   R ++MVFQSYALYPHM++ +NM F LKIAG+   EI   V  AA I
Sbjct: 61  DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKI 120

Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180
           L + HLL+R+P  LSGGQRQRVA+GRAI RQP VFLFDEPLSNLDA LR ++R E  KLH
Sbjct: 121 LHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLH 180

Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240
             ++ TMIYVTHDQ+EAMTL+D+IV++ +G IEQVG+P+ ++  PA +FVAGFIGSP MN
Sbjct: 181 DDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKMN 240

Query: 241 MEE----AVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDA 296
             +    A+  DG      G  L       S ++ GQKVT G+RP+         H   A
Sbjct: 241 FIDGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPE---------HLNIA 291

Query: 297 DAVHEIELPVTITEPLGNETLVFTQFNGRD--WVSRMLNPRPLRPGEAVPMSFDLARAHL 354
                ++   T  E LG+ + ++  + G +   + R+ +      G  +P++ D AR HL
Sbjct: 292 QGQAALQARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHL 351

Query: 355 FDGETGRAL 363
           F G  G+AL
Sbjct: 352 F-GADGQAL 359


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: 390
Number of extensions: 19
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: 372
Length adjustment: 30
Effective length of query: 335
Effective length of database: 342
Effective search space:   114570
Effective search space used:   114570
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