GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Halopiger salifodinae KCY07-B2

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_049992151.1 LT39_RS19510 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000784335.1:WP_049992151.1
          Length = 395

 Score =  264 bits (675), Expect = 3e-75
 Identities = 160/385 (41%), Positives = 225/385 (58%), Gaps = 28/385 (7%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA +KL  + K Y DV  + +++++I+ GE + FVGPSGCGKST +  +AGL + T G +
Sbjct: 1   MARVKLENITKRYDDVTAVDDVSMEIEDGEFVTFVGPSGCGKSTTMETVAGLTQPTEGQV 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            I    V ++ P  RG+AMVFQ+ AL+PHM V EN+SF L++ K    EI   VE AA+ 
Sbjct: 61  YIGNDDVTNLAPKDRGVAMVFQNIALFPHMNVFENISFGLRLRKYDDEEIQRRVEQAADI 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           +QL   LDR+P  +SGGQRQRVAI R+IVR+P V+L DEPL+NLDA LRV  R E+ +L 
Sbjct: 121 VQLEGMLDRMPDEMSGGQRQRVAIARAIVRNPDVFLMDEPLANLDAKLRVHMRTELQRLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + + ++T++YVTHDQ EAMT++ RI VL  G + Q+  PL  Y +P N FVA FIGSP M
Sbjct: 181 KEL-DTTIIYVTHDQAEAMTMSNRIAVLNKGRLQQLAPPLVCYNEPANLFVAGFIGSPSM 239

Query: 241 NLLPGKIIGTGAQT---TVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM-----VEAA 292
           N + G+++  G +T   TVE        +  P  D  +G AV +GVRPED+      ++ 
Sbjct: 240 NFVEGELVENGLETNNFTVEFDP-----THVP--DVSVGDAVTLGVRPEDVHLVQYADSL 292

Query: 293 PGGDYVFEGKVAITEALGE---VTLLYFEAPSG---EDPTIGK---LQGIHKDL---KGQ 340
                  + +  + E +G+   V LL  EA  G   EDP       L  +  D      Q
Sbjct: 293 SSPTDPIDAQTDVIEPMGDEVFVYLLLSEAAVGSMEEDPATSPNQLLMSVTPDTDIEADQ 352

Query: 341 VTRLTAEPAKVHVFKDGVSLHYPHG 365
              +  + +K+H+F         HG
Sbjct: 353 SVNVVLDRSKIHLFDTASGDALVHG 377


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: 368
Number of extensions: 16
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: 373
Length of database: 395
Length adjustment: 30
Effective length of query: 343
Effective length of database: 365
Effective search space:   125195
Effective search space used:   125195
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 24 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