GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Sinorhizobium meliloti 1021

Align RhaQ (characterized, see rationale)
to candidate SMc03001 SMc03001 ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__Smeli:SMc03001
          Length = 334

 Score =  454 bits (1169), Expect = e-132
 Identities = 235/326 (72%), Positives = 273/326 (83%), Gaps = 1/326 (0%)

Query: 7   QPEKRIIPDRLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEK 66
           Q   R IPDRL     R+  SWE LLF VA++IF+ NSLASPYFLD WNLSDATFNFTEK
Sbjct: 5   QISPRNIPDRLQGGGARLLKSWEALLFVVAIVIFLGNSLASPYFLDPWNLSDATFNFTEK 64

Query: 67  AMIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNG 126
           AMIAFAMAL++ISGEIDLSVA+IIALASTAMG AVQ+G  TP LV IG+G GL CG+ NG
Sbjct: 65  AMIAFAMALVIISGEIDLSVASIIALASTAMGYAVQLGFDTPALVAIGLGVGLLCGLVNG 124

Query: 127 VLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLF 186
           +L++ L LPSIVVTIGTMSLFRG+S+IVLGDQA+  YP  FA+FGQGYV WVFSFEF LF
Sbjct: 125 LLITGLGLPSIVVTIGTMSLFRGLSFIVLGDQAFTGYPESFAWFGQGYVWWVFSFEFTLF 184

Query: 187 IVLAVLFAILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLT 246
           +VLAV++ +LLH TNFGR VYAIGNN+ AA FSG+ V RVK  LFLLTG+M+G+A+VCLT
Sbjct: 185 VVLAVIYGVLLHRTNFGRAVYAIGNNETAALFSGVRVGRVKFTLFLLTGLMAGLASVCLT 244

Query: 247 SRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLP 306
           SRLGSTRPSIA GWELEVVTMVVLGG++ILGG     GV V+AA +MG+VTFG GLLN+P
Sbjct: 245 SRLGSTRPSIALGWELEVVTMVVLGGVNILGGSGTIPGV-VLAALIMGMVTFGFGLLNVP 303

Query: 307 GIVMSIFIGLLIIVTIAIPIIARRIK 332
           GIVMSIFIGLL+I  IA+PI+ +R +
Sbjct: 304 GIVMSIFIGLLLISVIALPILWQRAR 329


Lambda     K      H
   0.330    0.145    0.423 

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: 467
Number of extensions: 21
Number of successful extensions: 5
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: 337
Length of database: 334
Length adjustment: 28
Effective length of query: 309
Effective length of database: 306
Effective search space:    94554
Effective search space used:    94554
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: 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