GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Rhodobacter johrii JA192

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_069332736.1 C8J29_RS16565 ABC transporter permease

Query= uniprot:D8IZC8
         (344 letters)



>NCBI__GCF_003046325.1:WP_069332736.1
          Length = 330

 Score =  185 bits (469), Expect = 2e-51
 Identities = 125/328 (38%), Positives = 186/328 (56%), Gaps = 24/328 (7%)

Query: 29  LHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVIL 88
           LH LG  P+L +  L+  G  L        NF S  N  N+L + A   ++A GMTFVI 
Sbjct: 13  LHVLG--PLLALFVLIALGAWL------NPNFLSYGNVTNVLARSAFIGIIAVGMTFVIT 64

Query: 89  TAGIDLSVGSVLAVSAVLGMQVSLGAA---PGWAIPMFIF-------SGLVMGMVNGAMV 138
           + GIDLSVGS+ A  A L M +S+ A     G  + + +        +GL+ G +NG ++
Sbjct: 65  SGGIDLSVGSMAAFIAGL-MILSMNALLPHMGEGVSVILVGVLVAAGAGLLAGWLNGFLI 123

Query: 139 ALLNINAFVVTLGTMTAFRGAAYLLADGTTV-LNNDIPS-FEWIGNGDFLHVPWLIWVAV 196
           A + I  F+VTLGTM  +R     LADG T+ L+  +   +  +  G  L + W I V  
Sbjct: 124 AKVGIEPFIVTLGTMGIYRSLVTWLADGGTLSLDFGLRGLYRPVYYGGILGIAWPIIVFA 183

Query: 197 AVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSAS 256
            V +L  +++R+T  G H+ AIG N Q AR + ++V  V +  Y++ GL  GLA  M   
Sbjct: 184 IVAILGEIVMRQTAFGRHVAAIGANEQVARYSAVKVPRVRIATYALLGLLVGLATIMYVP 243

Query: 257 RLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGL-SS 315
           RL  A+G+ G  +EL+AIAAV++GGT L GG G +WGTVVG LI+ +++N L +  + S 
Sbjct: 244 RLGSASGSTGVLWELEAIAAVIIGGTVLKGGYGRVWGTVVGVLILSLIDNILNLASIVSP 303

Query: 316 FWQYVAKGAVIVLAVILDKWRQKDAAQS 343
           +     +G +++LAV+L   R+K AA +
Sbjct: 304 YLNGTIQGVIVILAVVLQ--REKKAADA 329


Lambda     K      H
   0.324    0.138    0.417 

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: 337
Number of extensions: 21
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: 344
Length of database: 330
Length adjustment: 28
Effective length of query: 316
Effective length of database: 302
Effective search space:    95432
Effective search space used:    95432
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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