GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natF in Sinorhizobium meliloti 1021

Align NatF, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate SMc00676 SMc00676 amino acid-binding periplasmic signal peptide protein

Query= TCDB::Q8YPM9
         (369 letters)



>FitnessBrowser__Smeli:SMc00676
          Length = 331

 Score =  317 bits (812), Expect = 3e-91
 Identities = 157/326 (48%), Positives = 213/326 (65%)

Query: 44  TSTNSGSTLVANRWNTIKNRGQLICGVSGEVPGFSFVGTDGEYSGIDVDVCRAIAAALFD 103
           T+  +G+T  A   + +K RG+L CGVS  V GFS     GE+SG D+D CRA+AAA   
Sbjct: 6   TAFLAGTTAQAATLDVVKQRGELRCGVSQGVLGFSAPDDKGEWSGFDIDFCRAVAAATLG 65

Query: 104 NPDAVEFRNLSAKERFTALQTGEVDILSRNTTWTLSRATSVGLEFAPVVFYDGQAIMVRK 163
           +PD V++  LS KERFTALQ+GEVD+LSR TTWTLSR T +G+ F  V +YDGQA MVR 
Sbjct: 66  SPDKVKYVPLSTKERFTALQSGEVDLLSRQTTWTLSRDTDLGMSFVGVNYYDGQAFMVRG 125

Query: 164 NSAIKSLADLKDKAICVQTGTTTEQNLADQMRKRNITYKPVVFEDVNVTFATYAEGRCDA 223
           +  +KS+ +L   ++C +TGTTTEQN+AD      I Y+ + FE  + T   +  GRCD 
Sbjct: 126 DIGVKSVKELSGASVCTETGTTTEQNMADYFSANKIEYQVIAFEKADQTIQAFNSGRCDV 185

Query: 224 ITADRSALVSRRTTLPTPEDNVVLDEVISSEPLAPAVARGDAKWSNTVNWVVYALIKGEE 283
            + D SAL S+R TL  P+  VVL EVIS EPL PAV +GD +W   V W ++A+I+ EE
Sbjct: 186 YSTDASALYSQRLTLNDPDRFVVLPEVISKEPLGPAVRQGDDQWFKVVRWTLFAMIEAEE 245

Query: 284 LGINAQNLGQFTTSNDPDVKRFLGTEGDLGQGLGLTNDFAARIIKHVGNYAEVYDRNLGP 343
           LGI  +N      S     KRFLG + + G+ LGL   +A + +  VGNY E+++R+LG 
Sbjct: 246 LGITRENAASLLESGTAAQKRFLGIDNEAGKALGLDPKWAYQTVAAVGNYGEIFERHLGK 305

Query: 344 KTKLNLARGQNQLWSKGGLLYSPPFR 369
           ++ L + RG N+LW+ GGL+Y+PP R
Sbjct: 306 ESALRIDRGLNKLWNNGGLIYAPPVR 331


Lambda     K      H
   0.317    0.133    0.387 

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: 366
Number of extensions: 13
Number of successful extensions: 1
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: 369
Length of database: 331
Length adjustment: 29
Effective length of query: 340
Effective length of database: 302
Effective search space:   102680
Effective search space used:   102680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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