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_RS05835 HSERO_RS05835 arginine ABC transporter ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>FitnessBrowser__HerbieS:HSERO_RS05835
          Length = 242

 Score =  254 bits (649), Expect = 1e-72
 Identities = 138/248 (55%), Positives = 168/248 (67%), Gaps = 12/248 (4%)

Query: 6   LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65
           + V  + K +G HEVLK VSL    G+V+ +IG SGSGKST LRCIN LE    G I+++
Sbjct: 2   IEVKRISKCFGRHEVLKDVSLSVAQGEVVCLIGPSGSGKSTVLRCINGLESYERGDILID 61

Query: 66  GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125
           GQ +    D+DG         +  LRTR+ MVFQ FNL+ H TVLENV E PI V GL++
Sbjct: 62  GQRV----DRDGP-------DIHRLRTRVGMVFQRFNLFPHRTVLENVTEGPIYVNGLAR 110

Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185
            +AR  A+  L KVG+  R    YP  LSGGQQQRV+IAR+LAM+PE +LFDEPTSALDP
Sbjct: 111 AQARSEAMSLLDKVGLAARCDA-YPAQLSGGQQQRVAIARSLAMQPEAILFDEPTSALDP 169

Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245
           ELVGEVL +M+ LA +G TM+VVTHEMGFAR V+  V FLH G I E GA  Q+   PQ 
Sbjct: 170 ELVGEVLAVMRTLAADGMTMIVVTHEMGFAREVADRVCFLHSGSIVESGAAAQVLAEPQH 229

Query: 246 PRLQRFLK 253
            R Q FL+
Sbjct: 230 ARTQDFLR 237


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: 197
Number of extensions: 4
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: 242
Length adjustment: 24
Effective length of query: 233
Effective length of database: 218
Effective search space:    50794
Effective search space used:    50794
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: 46 (22.3 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