GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Herbaspirillum seropedicae SmR1

Align histidine transport ATP-binding protein hisP (characterized)
to candidate HSERO_RS11450 HSERO_RS11450 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>FitnessBrowser__HerbieS:HSERO_RS11450
          Length = 257

 Score =  231 bits (590), Expect = 9e-66
 Identities = 127/256 (49%), Positives = 175/256 (68%), Gaps = 7/256 (2%)

Query: 1   MSENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEG 60
           M+E  + V  L K +G H VLK + L      V+ +IG SGSGKSTFLRC+N LEK   G
Sbjct: 1   MTEPIVEVSGLRKSFGAHVVLKDLDLSVAPSQVVVVIGPSGSGKSTFLRCLNGLEKAEGG 60

Query: 61  SIVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV 120
           ++ V G+ +      +G  ++  +  L LLR  + MVFQ FNL+ H+TVL+N+  AP  +
Sbjct: 61  TVKVCGRPV-----VEGG-RMMPEAMLDLLRAEVGMVFQSFNLFPHLTVLDNITLAPTCL 114

Query: 121 LGLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180
            G+S++ A+++A++ L KVG+  +A+  YP  LSGGQ+QRV+IARALAMEP+V+LFDEPT
Sbjct: 115 RGMSRKAAQQQALQLLEKVGLAHKAKA-YPGTLSGGQKQRVAIARALAMEPQVMLFDEPT 173

Query: 181 SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLF 240
           SALDPELVGEVL++++ LA EG TM++VTHEMGFAR V+  V+ +  G I E G P  +F
Sbjct: 174 SALDPELVGEVLQVIRALAAEGMTMIIVTHEMGFAREVADVVVVMDHGSIVEAGPPGAIF 233

Query: 241 GNPQSPRLQRFLKGSL 256
             PQ  R + FL+  L
Sbjct: 234 TAPQQARTRSFLQTML 249


Lambda     K      H
   0.318    0.134    0.375 

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: 208
Number of extensions: 7
Number of successful extensions: 3
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: 257
Length of database: 257
Length adjustment: 24
Effective length of query: 233
Effective length of database: 233
Effective search space:    54289
Effective search space used:    54289
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: 47 (22.7 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