GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Klebsiella michiganensis M5al

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease

Query= reanno::acidovorax_3H11:Ac3H11_2943
         (316 letters)



>FitnessBrowser__Koxy:BWI76_RS03135
          Length = 290

 Score = 98.2 bits (243), Expect = 2e-25
 Identities = 84/286 (29%), Positives = 138/286 (48%), Gaps = 13/286 (4%)

Query: 30  MNRRLLPRLLLTPAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEFFVTDP 89
           M +  LP L+L+P++  L L+   PL  ++Y SL    ++  D   + GLENF     D 
Sbjct: 1   MRKTWLPWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVS-DGGQYVGLENFSRLFADS 59

Query: 90  SFGTAVVNTILLLGSVILITVVLGVAIALLINEPFPGRGIVRVLLISPFF---VMPTVNA 146
            F  ++VN +L     IL+TVV GV +ALL+         V   L + FF   ++P V+A
Sbjct: 60  VFWQSLVNNLLY----ILLTVVPGVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVSA 115

Query: 147 LMWKNMMMNPIYGVLAQVWI-FFGAAPVDWL--TDHPLFSVIVMVSWQWLPFATLIFMTA 203
                 +  P  G+L       FG    +WL  ++  L ++ ++  W++  +  L F+  
Sbjct: 116 AALWLFIFMPGLGLLDHYLAKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAG 175

Query: 204 LQSMNHEQLEASRMDGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGG 263
           LQS+     EA+ M+GA   Q    + +P L  +++ V+   LI+ ++    +   T GG
Sbjct: 176 LQSIPASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTRGG 235

Query: 264 PGDASTNVTFLIFKQALLNFDAGVASAGALFAVVLANIAAVFLIRM 309
           P +A+T + + I   A    D G ASA     + LA + A  LI +
Sbjct: 236 PDNATTVLLYYIQNLAWDTHDLGKASAATF--LTLAGLFAFSLINL 279


Lambda     K      H
   0.331    0.142    0.436 

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: 264
Number of extensions: 15
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: 316
Length of database: 290
Length adjustment: 27
Effective length of query: 289
Effective length of database: 263
Effective search space:    76007
Effective search space used:    76007
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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