GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Herbaspirillum seropedicae SmR1

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__HerbieS:HSERO_RS22750
          Length = 377

 Score =  327 bits (838), Expect = 3e-94
 Identities = 188/358 (52%), Positives = 237/358 (66%), Gaps = 9/358 (2%)

Query: 1   MADLKLTGVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59
           MA + +  + K Y G   VL+ +NLDI+ GE  V VGPSGCGKSTLLRM+ GLE+I+GG 
Sbjct: 1   MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60

Query: 60  LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           L I G VVN +PPA+RGIAMVFQSYALYPHM V +NM+F LK+A  S+++IDA +  AA 
Sbjct: 61  LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVAGNSKSDIDARIRHAAA 120

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            L++   L RLP+ LSGGQRQRVAIGR+IVR P+++LFDEPLSNLDAALRV TRLEIA+L
Sbjct: 121 ILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAKL 180

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
              +  +T+VYVTHDQVEAMTL  +IVV+  G I Q G+PLELY++P+N FVA FIGSPK
Sbjct: 181 HRQL-AATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPK 239

Query: 240 MNLLPGKII---GTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGD 296
           MN   G +     +G Q  VE+  G R ++D        GAAV +G+R E + E   G  
Sbjct: 240 MNFFQGVVTRCDDSGVQ--VEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREGL-GDG 296

Query: 297 YVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
               G V + E LGE   LY     G D  +      + D+ GQ   L+      H+F
Sbjct: 297 QPLHGVVNLVEHLGEANFLYVTLDGGHDIVVRGDGNRNVDI-GQPIALSVHSHAFHLF 353


Lambda     K      H
   0.316    0.135    0.379 

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: 434
Number of extensions: 20
Number of successful extensions: 4
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: 373
Length of database: 377
Length adjustment: 30
Effective length of query: 343
Effective length of database: 347
Effective search space:   119021
Effective search space used:   119021
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 (21.6 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