GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Desulfacinum infernum DSM 9756

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  399 bits (1024), Expect = e-116
 Identities = 201/369 (54%), Positives = 265/369 (71%), Gaps = 4/369 (1%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA + L+ + K +  +    V+DF L + DKEF V VGPSGCGK+TTLRMIAGLE++T G
Sbjct: 1   MAEIKLDQVNKRF--KKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            + IG R VN VPPKDRDIAMVFQ+YALYPHM VY+NMAFGL  R VP+ EIDRRV++AA
Sbjct: 59  EISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAA 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           +IL I+ LL R+P  LSGGQRQRVA+GRAIVR+PQ FL DEPLSNLDAKLRVQMRAE+ K
Sbjct: 119 EILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAK 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LH+RLQ+T++YVTHDQ EAMT+ DRIVVM+DG I Q   P  VY +P N FVAGFIGSP+
Sbjct: 179 LHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPS 238

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300
           MNF+   +V++    +    S  L++P  R    +  G + +PV+ G+RPED+ +     
Sbjct: 239 MNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFR--GHVNRPVIFGIRPEDVKERPGDA 296

Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHI 360
                  L+ +V+V E +GSEV +  ++G +   AR++P     V   + LA+++NK+H+
Sbjct: 297 LPEGVEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHL 356

Query: 361 FDAETEESI 369
           FD E+E+++
Sbjct: 357 FDPESEQAL 365


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: 466
Number of extensions: 15
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: 384
Length of database: 368
Length adjustment: 30
Effective length of query: 354
Effective length of database: 338
Effective search space:   119652
Effective search space used:   119652
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 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