GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Caldicellulosiruptor kronotskyensis 2002

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_013429917.1 CALKRO_RS04555 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000166775.1:WP_013429917.1
          Length = 370

 Score =  501 bits (1291), Expect = e-146
 Identities = 252/369 (68%), Positives = 295/369 (79%), Gaps = 1/369 (0%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA V L+ +YK YPG     V DFNLDI+DKEF V VGPSGCGKTTTLRMIAGLE++TEG
Sbjct: 1   MASVRLKGVYKRYPGGVT-AVSDFNLDIEDKEFIVLVGPSGCGKTTTLRMIAGLEEVTEG 59

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            +YIGD+ VNDVPPKDRDIAMVFQNYALYPHMTV++NMAFGLKLRK PK EI RRV EAA
Sbjct: 60  EIYIGDKLVNDVPPKDRDIAMVFQNYALYPHMTVFENMAFGLKLRKFPKDEIKRRVHEAA 119

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           KIL I HLLDRKPKALSGGQRQRVALGRAIVREP+VFLMDEPLSNLDAKLRVQMRAE+ K
Sbjct: 120 KILGIEHLLDRKPKALSGGQRQRVALGRAIVREPKVFLMDEPLSNLDAKLRVQMRAELSK 179

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LH+RL TT IYVTHDQTEAMTMG RIVVM+DG IQQ DTPQV+Y QP N+FVAGFIGSP 
Sbjct: 180 LHKRLGTTFIYVTHDQTEAMTMGTRIVVMKDGFIQQVDTPQVLYEQPANLFVAGFIGSPQ 239

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300
           MNFI   I Q     Y    + +++LPEG+   ++  G +GK V++G+RPEDLHDEE+F+
Sbjct: 240 MNFIESRIEQKDKNLYVVFGNNAIKLPEGKAKKVEELGYVGKEVIMGIRPEDLHDEEIFL 299

Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHI 360
            T  D+V+   V+VVE +GSE  L+  +    ++ARV+PR     G  +KLA D+N+IH+
Sbjct: 300 QTAQDAVVDADVDVVEMLGSETLLYVVVDGLNLIARVDPRSKAKSGDKIKLAFDVNRIHL 359

Query: 361 FDAETEESI 369
           FD ETE++I
Sbjct: 360 FDKETEKAI 368


Lambda     K      H
   0.321    0.138    0.395 

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: 510
Number of extensions: 16
Number of successful extensions: 2
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: 384
Length of database: 370
Length adjustment: 30
Effective length of query: 354
Effective length of database: 340
Effective search space:   120360
Effective search space used:   120360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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