GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Thiothrix lacustris DSM 21227

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  290 bits (743), Expect = 3e-83
 Identities = 175/371 (47%), Positives = 224/371 (60%), Gaps = 43/371 (11%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA + L+++ K Y G+    +K  +L+IQ  EF VFVGPSGCGK+T LRMIAGLE I  G
Sbjct: 1   MAFLELKNVDKYY-GKLH-AIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            L +  R + +VPP  RD+AMVFQ+YALYPHMTV +NM+F L+L KV  A I  +V+ AA
Sbjct: 59  QLILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAA 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
             L++   L R PKALSGGQRQRVA+GR+IVR P+VFL DEPLSNLDA LR   R EI  
Sbjct: 119 DKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIAS 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LH+ L  T +YVTHDQ EAMT+ DR+VV+RDG+I+Q  TP  +Y QP N FVA FIG P 
Sbjct: 179 LHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQ 238

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300
           MN                        P   +G   A  A      +G+RPE L      M
Sbjct: 239 MNV----------------------APASLFGQFPAQVA-----EVGIRPEHLQ-----M 266

Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTI------VARVNPRHVYHVGSSVKLAID 354
            +  D +L  +V +VE +G+E  +H  + P+ +      + R+  R   HVG  V L  D
Sbjct: 267 VSPEDGLLAGKVVLVEALGNETLVH--VRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWD 324

Query: 355 LNK-IHIFDAE 364
            +K IH FD +
Sbjct: 325 DSKHIHYFDTK 335


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: 397
Number of extensions: 14
Number of successful extensions: 1
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: 348
Length adjustment: 30
Effective length of query: 354
Effective length of database: 318
Effective search space:   112572
Effective search space used:   112572
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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