GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Herbaspirillum seropedicae SmR1

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>FitnessBrowser__HerbieS:HSERO_RS22750
          Length = 377

 Score =  320 bits (821), Expect = 3e-92
 Identities = 181/361 (50%), Positives = 230/361 (63%), Gaps = 24/361 (6%)

Query: 1   MAGIKIDKINKFY-GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59
           MA + I ++ K Y G    L  +NLDI DGEF V VGPSGCGKSTLLR L GLE +S G 
Sbjct: 1   MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60

Query: 60  IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119
           + IGG+ V  + PA+R +AMVFQSYALYPHM V +NM FG+KV G        RI  AA 
Sbjct: 61  LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120

Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179
           +L+++  L R P +LSGGQRQRVAIGRAIV+ P +FLFDEPLSNLDA LRVQ R+E+  L
Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180

Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239
           H+QL AT++YVTHDQVEAMT+ DKIVV++ GRI+Q G+P++LY +P + FVA FIGSP M
Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240

Query: 240 NVFS------SDVGLQ-----------DIS----LDASAAFVGCRPEHI-EIVPDGDGHI 277
           N F        D G+Q           D+        +A  +G R E I E + DG   +
Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGLGDGQ-PL 299

Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRA 337
              V++ E LG  + LY+ L GG  IV R  G+    +G  ++L    H  H FD  G+A
Sbjct: 300 HGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFDAQGQA 359

Query: 338 I 338
           +
Sbjct: 360 L 360


Lambda     K      H
   0.320    0.139    0.396 

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: 393
Number of extensions: 13
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: 338
Length of database: 377
Length adjustment: 29
Effective length of query: 309
Effective length of database: 348
Effective search space:   107532
Effective search space used:   107532
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