GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Herbaspirillum seropedicae SmR1

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__HerbieS:HSERO_RS22750
          Length = 377

 Score =  301 bits (770), Expect = 2e-86
 Identities = 172/355 (48%), Positives = 227/355 (63%), Gaps = 18/355 (5%)

Query: 1   MAKIQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59
           MA +    ++K++ G ADVL G++LDI  GEF VLVGPSGCGKSTLLR L GLE    G 
Sbjct: 1   MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60

Query: 60  ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119
           ++I G+ +N + P  R IAMVFQSYALYPHM V +NM FGLK+   + ++I  R+   + 
Sbjct: 61  LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120

Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179
           +L+I HLL R P+ELSGGQRQRVA+GRA+ RQ  + LFDEPLSNLDA LR Q RLEI +L
Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180

Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239
           H    +T++YVTHDQ+EA TLGD+I V+ +G I+Q GTP E+Y +P+N F+A FIGSP+M
Sbjct: 181 HRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPKM 240

Query: 240 NFLEGAVLE--------KIPWPEARKAD-QILGIRPDAFALNQGPLGTQ-EVALGDFQ-- 287
           NF +G V          +I       AD   LG+ P A A+  G    Q    LGD Q  
Sbjct: 241 NFFQGVVTRCDDSGVQVEIAGGLRLLADVDPLGVTPGA-AVTLGLRAEQIREGLGDGQPL 299

Query: 288 ---IDISENLGGQQMLHGTL-AGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFD 338
              +++ E+LG    L+ TL  G+++ +  D   N  + Q + L +     HLFD
Sbjct: 300 HGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSHAFHLFD 354


Lambda     K      H
   0.318    0.136    0.383 

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: 355
Number of extensions: 15
Number of successful extensions: 1
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: 347
Length of database: 377
Length adjustment: 29
Effective length of query: 318
Effective length of database: 348
Effective search space:   110664
Effective search space used:   110664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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