GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Herbaspirillum seropedicae SmR1

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__HerbieS:HSERO_RS01335
          Length = 283

 Score =  141 bits (355), Expect = 3e-38
 Identities = 82/229 (35%), Positives = 126/229 (55%), Gaps = 6/229 (2%)

Query: 151 LDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGL 210
           L+NY E L+A+ +   F NS  + +PS +  I +AA A +AL+   F G  VL A  V  
Sbjct: 61  LENYREALTASPMLHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATFVAC 120

Query: 211 LVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREI 270
             VP Q+ +IP+  L   +G F      T  G+ L H           LRN++  LP E+
Sbjct: 121 NFVPQQILMIPVRDLSLSLGLF-----NTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEM 175

Query: 271 MESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTG 330
           +E+AR++GAS++ +F +I+LPL  PALA+ A+  F + WND   A+V L  GDD   +T 
Sbjct: 176 IEAARIEGASEWTVFYRIVLPLIRPALAALAVLVFTFVWNDYFWALV-LTQGDDVAPITV 234

Query: 331 RLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
            +  L G     W +++A + +  +  +I+FF +Q+  V GL  G+ KG
Sbjct: 235 GVAALRGQWTTAWNLVSAGSILAALPSVILFFVMQKQFVAGLTFGASKG 283



 Score = 32.3 bits (72), Expect = 2e-05
 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 5/53 (9%)

Query: 16 SVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWW-----TALSSSSRNAVVRAP 63
          S+ + +L+W LP    L++S+R  D+L    +W      A+  + R A+  +P
Sbjct: 20 SLPVALLIWLLPMLAALVTSIRSNDELMAGNYWGWPQDFAMLENYREALTASP 72


Lambda     K      H
   0.324    0.139    0.418 

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: 253
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 380
Length of database: 283
Length adjustment: 28
Effective length of query: 352
Effective length of database: 255
Effective search space:    89760
Effective search space used:    89760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 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