GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Sinorhizobium meliloti 1021

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate SMc03063 SMc03063 alpha-glucoside ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Smeli:SMc03063
          Length = 380

 Score =  447 bits (1149), Expect = e-130
 Identities = 227/383 (59%), Positives = 289/383 (75%), Gaps = 15/383 (3%)

Query: 8   KSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNLTLRAADP 67
           +S LTWAV LSV+ LV+LW LPT GL +SS R  +Q++ SGWW A+  S +N  +RA   
Sbjct: 6   RSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVVRAPSA 65

Query: 68  DDFRMPQGDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGETITVQSN 127
           +D ++ +   FV+ GNL E  G    E+S +G SSR+   +  GETA+L DGE +TVQS+
Sbjct: 66  ED-QVERDGKFVISGNLLEGRG----EVSAFGFSSREPTKFKPGETAELNDGERLTVQSD 120

Query: 128 GAYVWSGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIP 187
           G++           RGQR+F TATTPP FT  NY  +L    ++ G+ R+F N+LTV +P
Sbjct: 121 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVL----SAAGIGRSFLNSLTVAVP 176

Query: 188 ATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAIGI----- 242
           +T+IPIL+AAFAAYALAWM FPGRA+L+A++VGLLVVPLQ++LIPLL L+N +G      
Sbjct: 177 STVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVS 236

Query: 243 GKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPA 302
            K Y+G WLAHTGFG+PLAIYLLRNYM GLPR+I+E+A+VDGA+DF IF KI+LPLSFPA
Sbjct: 237 AKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPA 296

Query: 303 LASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIA 362
           LASFAIFQFLWTWNDLLVA VFL  A     V+T ++V LLG+RGGNWEIL  +AF++I 
Sbjct: 297 LASFAIFQFLWTWNDLLVAIVFL-GAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIV 355

Query: 363 VPLLVFFSMQRFLVRGLLAGSVK 385
           VPL+VFF++QR+LVRGLLAGSVK
Sbjct: 356 VPLIVFFALQRYLVRGLLAGSVK 378


Lambda     K      H
   0.323    0.138    0.419 

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: 450
Number of extensions: 17
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: 385
Length of database: 380
Length adjustment: 30
Effective length of query: 355
Effective length of database: 350
Effective search space:   124250
Effective search space used:   124250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 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