GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Cronobacter universalis NCTC 9529

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate WP_038857748.1 AFK65_RS05695 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>NCBI__GCF_001277175.1:WP_038857748.1
          Length = 371

 Score =  201 bits (510), Expect = 3e-56
 Identities = 120/327 (36%), Positives = 186/327 (56%), Gaps = 26/327 (7%)

Query: 26  PLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQV 85
           PL ++   G    ++GPSGCGK+T+L +++GL   + G +  D + V   SP ER I  V
Sbjct: 22  PLDLQINSGEFVVVVGPSGCGKSTLLRLVAGLEEITDGDMYIDDQRVNDDSPSERGIGMV 81

Query: 86  FQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQ 145
           FQ   +Y  MTV +N+AF L   KVPE +I +RV   A +L++   L++R   L+   +Q
Sbjct: 82  FQSYALYPHMTVYQNMAFALEMAKVPEKEIDERVRESARILQLEHLLDRRPKDLSGGQRQ 141

Query: 146 KISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALT 205
           ++++GR +VR + +  LFDEPL+ +D  L+ Q+R ++  +H  +  T++YVTHDQVEA+T
Sbjct: 142 RVAIGRAIVR-EPSLFLFDEPLSNLDASLRVQMRMEIAALHRRIHATILYVTHDQVEAMT 200

Query: 206 FADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGH--- 262
            AD++VV+ +G+  QVG+  AL++ PA+ FV  FIGSP MN +P    G+ L V  H   
Sbjct: 201 LADRIVVLNQGQIEQVGTPLALYDTPANVFVAQFIGSPKMNLIP----GKMLRVMEHACE 256

Query: 263 -------RLASPVGRAL--PAGALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQML 313
                  RL  PV         A+Q+GIRPE++ +    +A  + G V+ V+ +G   ++
Sbjct: 257 VELENGLRLTLPVQAVAGQEGDAVQLGIRPEHVEIMTLAKAD-VEGEVLFVEHMGNETLV 315

Query: 314 TAKVG--------EHTVKARFTPETRL 332
               G         HT +    PE  L
Sbjct: 316 YVNGGYGAEPLVMRHTERLEVRPEHHL 342


Lambda     K      H
   0.320    0.136    0.395 

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: 323
Number of extensions: 14
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: 358
Length of database: 371
Length adjustment: 29
Effective length of query: 329
Effective length of database: 342
Effective search space:   112518
Effective search space used:   112518
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: 49 (23.5 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