GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Pseudomonas stutzeri RCH2

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__psRCH2:GFF139
          Length = 257

 Score =  213 bits (542), Expect = 3e-60
 Identities = 110/247 (44%), Positives = 160/247 (64%), Gaps = 13/247 (5%)

Query: 2   IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV- 60
           +E++N++K YG   VLK I+L+ ++G+ + I+G SGSGKST +RC+N LE    GE++V 
Sbjct: 8   LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEILVA 67

Query: 61  -----------NNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSK 109
                       +LV     ++   R     VFQ+FNL+PHMT+L N+  AP ++  +SK
Sbjct: 68  GEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQSK 127

Query: 110 KEAEETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPE 169
            EA E A   L  VG+ DK +VYP  LSGGQQQR AIAR+L  +   ILFDEPTSALDPE
Sbjct: 128 AEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187

Query: 170 TIQEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKT 229
            +QEVL V++ ++ +   TM++VTHEM FAK+V+  ++F+  G + E+  P + F NP++
Sbjct: 188 MVQEVLAVIRSLAEEGR-TMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQS 246

Query: 230 ERARLFL 236
            R + F+
Sbjct: 247 ARCKQFM 253


Lambda     K      H
   0.317    0.133    0.372 

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: 161
Number of extensions: 5
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: 242
Length of database: 257
Length adjustment: 24
Effective length of query: 218
Effective length of database: 233
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