GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Pseudomonas stutzeri RCH2

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__psRCH2:GFF3786
          Length = 295

 Score =  145 bits (365), Expect = 1e-39
 Identities = 99/299 (33%), Positives = 166/299 (55%), Gaps = 18/299 (6%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60
           ++ FL QL+ GL  G+ Y ++++G  +++G++ +INFAHG  YMIGAF     +L + +L
Sbjct: 9   IQAFLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAG---YLLLATL 65

Query: 61  GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120
           GI + P  +L  ++   L +AV    +ER+A   L +   L  L+   G+++ L+   + 
Sbjct: 66  GIGYWPALILAPIIVG-LCSAV----IERLALSRLYNLDHLYSLLFTFGLALALEGAFRY 120

Query: 121 LQGARSKP--LQPILPG--NLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRA 176
             G+  +P  +   L G  NL  M      ++V LA++VI IA       LI +T LG  
Sbjct: 121 FYGSSGQPYAVPKELAGGYNLGFMFLPKYRAWVVLASLVICIASWL----LIEKTKLGAY 176

Query: 177 QRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAF 236
            RA  ++  +    G+NV  +++ T+ MGAALA +AGM+   IY V    +G    +  F
Sbjct: 177 LRAATENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQVSPL-MGSNLIIVVF 235

Query: 237 TAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295
              V+GG+GS+ GA++ G ++G++E     +   E  ++  F I+ +VL+ RP GL+GR
Sbjct: 236 AVVVVGGMGSILGAIITGYMLGILEGLTKVFY-PEASNIVIFVIMAIVLLVRPAGLMGR 293


Lambda     K      H
   0.329    0.144    0.425 

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: 320
Number of extensions: 15
Number of successful extensions: 5
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: 301
Length of database: 295
Length adjustment: 26
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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