GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisP in Herbaspirillum seropedicae SmR1

Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS17555 HSERO_RS17555 arginine ABC transporter ATP-binding protein

Query= uniprot:Q88GX0
         (260 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS17555 HSERO_RS17555 arginine
           ABC transporter ATP-binding protein
          Length = 244

 Score =  258 bits (660), Expect = 6e-74
 Identities = 130/242 (53%), Positives = 173/242 (71%), Gaps = 2/242 (0%)

Query: 20  LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79
           +I ++ ++K+YG F VL   +  + +GE +V+CGPSGSGKSTLI+ IN LE  Q+GSI +
Sbjct: 1   MITLQDVSKYYGDFKVLSACNAVIAKGEVVVVCGPSGSGKSTLIKTINALEPIQEGSITI 60

Query: 80  DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139
           DG+ +   +    ++RS +GMVFQHF LFPH++++ N  LA   V G  + +A +    Y
Sbjct: 61  DGVKVNDRSTNLPRLRSRVGMVFQHFELFPHLTIIQNLTLAQIKVLGRKKDEAHQHGMKY 120

Query: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199
           L +VG+++ A KYP QLSGGQQQRVAIARAL M P  MLFDEPTSALDPEMV EVLDV+V
Sbjct: 121 LERVGLKAHAGKYPGQLSGGQQQRVAIARALAMDPICMLFDEPTSALDPEMVNEVLDVMV 180

Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFF--NQPRTERAKAFLAQ 257
           +LA  GMTM+CVTHEMGFAR VA RV+F++ G I+ED     FF      + R++ FL++
Sbjct: 181 ELAQEGMTMVCVTHEMGFARMVAHRVIFMDQGSIVEDRSKDDFFAGGGDHSARSRQFLSK 240

Query: 258 IL 259
           IL
Sbjct: 241 IL 242


Lambda     K      H
   0.322    0.137    0.395 

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: 189
Number of extensions: 5
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: 260
Length of database: 244
Length adjustment: 24
Effective length of query: 236
Effective length of database: 220
Effective search space:    51920
Effective search space used:    51920
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 (21.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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