GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Rhodobacter viridis JA737

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_110804296.1 C8J30_RS02695 ABC transporter ATP-binding protein

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



>NCBI__GCF_003217355.1:WP_110804296.1
          Length = 358

 Score =  155 bits (393), Expect = 9e-43
 Identities = 93/247 (37%), Positives = 140/247 (56%), Gaps = 16/247 (6%)

Query: 15  LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74
           ++E   +HK YG    L+G+  T++ G   +L+G SG GKTTLLR +   E+   G +L+
Sbjct: 1   MIEFDRVHKYYGDYHALRGITATIREGEFFSLLGPSGCGKTTLLRTIAGFEDISSGSVLI 60

Query: 75  DGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134
           DG             +H E V    R  T M FQ + +FPHL+  QNV  GL +  +   
Sbjct: 61  DG-------------KHMEDVPPNKRP-TNMVFQSYAIFPHLSVGQNVGFGLRRDPRSEA 106

Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194
           ++A  + E+ LE VGL          LSGGQ+QRVA+ARA+ + P ++L DE  SALD +
Sbjct: 107 EKAKAV-EEALEMVGLKGYGARAAHALSGGQRQRVALARALILKPKVLLLDEPLSALDKK 165

Query: 195 LVGEV-LSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 253
           +  ++ + +IK   E G+T +LVTH+   A  +SD+I  M +G I +   P+ L+ RP S
Sbjct: 166 IREQMQIELIKLQREVGITFVLVTHDQEEALVMSDRIAVMFEGEIAQLADPETLYRRPAS 225

Query: 254 PRLAEFL 260
            R+A+F+
Sbjct: 226 RRVADFI 232


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: 212
Number of extensions: 9
Number of successful extensions: 4
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: 358
Length adjustment: 27
Effective length of query: 238
Effective length of database: 331
Effective search space:    78778
Effective search space used:    78778
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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