GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Sinorhizobium fredii NGR234

Align LacF, component of Lactose porter (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= TCDB::P29823
         (298 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  148 bits (373), Expect = 2e-40
 Identities = 99/296 (33%), Positives = 156/296 (52%), Gaps = 19/296 (6%)

Query: 4   TSRSSLKRYYDVNGW-------LFVAPAIALISVFMLYPILRSLVLSLYT---GRGMMLK 53
           TS  SL+R   +  W       L +AP + ++    ++P +     +++       +  +
Sbjct: 8   TSAKSLRRGGGLEHWAERHLRYLMLAPTVLILLALTIFPSIYMFYAAVHRISPNPDLPWE 67

Query: 54  FSGTGNLVRLWNDPVFWQALQNTVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMI 113
           F G GN  RL +DP F  AL+NTV+F +V V +   + L LA +L+    R S L +T++
Sbjct: 68  FVGVGNFARLLSDPQFHVALRNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFL-KTVL 126

Query: 114 FLPCVSSLVAYSILFKSMFSLD-GVVNNTLLAIGIIGEPI-GWLTDPFWAKVLIIIAITW 171
            +P +   +A +I +K ++    GV+N  +  +G+   P+  W  D   A   II+A  W
Sbjct: 127 MIPMMLPPIAVAITWKLIYEPQFGVLNEIMFLLGL---PVQAWAGDVNLAMFSIIVADVW 183

Query: 172 RWTGYNMIFYLAALQNIDRSIYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTL 231
           +WT +  +  LA L ++    YEAA +DG  SW +F  LT+P LKPVI    +   +  L
Sbjct: 184 QWTPFVFLLMLAGLASLPVEPYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDAL 243

Query: 232 QLFDEVYNFTEGTGGPANSTLTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLS 287
           +LFD V+  T   GGPA+ T  LSLYIY + +RF     YAA +S  ++ +  VLS
Sbjct: 244 RLFDLVFILT--GGGPADRTKVLSLYIYQVAYRFADP-GYAAAISLFVLFVTIVLS 296


Lambda     K      H
   0.329    0.141    0.435 

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: 267
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: 298
Length of database: 307
Length adjustment: 27
Effective length of query: 271
Effective length of database: 280
Effective search space:    75880
Effective search space used:    75880
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 Apr 09 2024. 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