GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate HSERO_RS19345 HSERO_RS19345 amino acid ABC transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS19345
          Length = 244

 Score =  248 bits (634), Expect = 7e-71
 Identities = 128/250 (51%), Positives = 176/250 (70%), Gaps = 11/250 (4%)

Query: 14  ALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIL 73
           A+++I+DLHK +G  +VL GV L +Q+G +V +IG SGSGK+TLLRC+N LE+   G I 
Sbjct: 3   AIVKIKDLHKSFGSNKVLNGVSLDVQKGQMVAIIGKSGSGKSTLLRCLNGLEKVDAGDI- 61

Query: 74  LDGESIGYHEVNGKRVRHSEKV-IAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 132
                    +V G  + H +K+ + + R   G+ FQ +NLFPHLT  +N+TL L  +KK+
Sbjct: 62  ---------QVCGHDIHHPDKLNLRELRKQVGIVFQSYNLFPHLTVERNITLALTTIKKM 112

Query: 133 HKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192
             ++A  +A K L+ VGL  ++D YP QLSGGQ QRVAIAR++AM P LMLFDEVTSALD
Sbjct: 113 STEQAKTIAHKVLQLVGLENKKDAYPEQLSGGQAQRVAIARSLAMAPELMLFDEVTSALD 172

Query: 193 PELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQ 252
           PEL  EVL V++ LA  GMTM+LVTHEM FA +++D +VFM+QG++ E GPP ELF  P+
Sbjct: 173 PELTAEVLKVMEDLARGGMTMVLVTHEMAFARKLADVLVFMHQGQVWEIGPPDELFSHPK 232

Query: 253 SPRLAEFLKN 262
           +  L +F+ +
Sbjct: 233 TAELQKFVSS 242


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: 178
Number of extensions: 8
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: 244
Length adjustment: 24
Effective length of query: 241
Effective length of database: 220
Effective search space:    53020
Effective search space used:    53020
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 (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