GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_21725 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>lcl|FitnessBrowser__psRCH2:GFF139 Psest_0139 ABC-type histidine
           transport system, ATPase component
          Length = 257

 Score =  256 bits (654), Expect = 3e-73
 Identities = 131/250 (52%), Positives = 179/250 (71%), Gaps = 1/250 (0%)

Query: 16  LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75
           LEIR+LHK+YG LEVLKG+ LT + G+V++++GSSGSGK+T LRC+N+LE    G+IL+ 
Sbjct: 8   LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEILVA 67

Query: 76  GESIGY-HEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134
           GE +    +  G  V    K + + R+  G  FQ FNL+PH+T L N+     +V    K
Sbjct: 68  GEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQSK 127

Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194
            EA  +AE  L +VG+ ++R  YP QLSGGQQQR AIAR +AM P ++LFDE TSALDPE
Sbjct: 128 AEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187

Query: 195 LVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 254
           +V EVL+VI+ LAE+G TMLLVTHEM FA +VS ++VF++QG +EEQG P+++F+ PQS 
Sbjct: 188 MVQEVLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQSA 247

Query: 255 RLAEFLKNTR 264
           R  +F+ + R
Sbjct: 248 RCKQFMSSHR 257


Lambda     K      H
   0.319    0.135    0.379 

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: 199
Number of extensions: 9
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: 265
Length of database: 257
Length adjustment: 25
Effective length of query: 240
Effective length of database: 232
Effective search space:    55680
Effective search space used:    55680
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: 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 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