GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Brucella inopinata BO1

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000182725.1:WP_008509836.1
          Length = 333

 Score =  280 bits (716), Expect = 4e-80
 Identities = 165/364 (45%), Positives = 221/364 (60%), Gaps = 39/364 (10%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA + L  + K++ G  E  +K  ++DI+  EF VFVGPSGCGK+T LR+IAGLE+IT G
Sbjct: 1   MAELQLRDVRKSF-GSFE-VIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
            L I    VN+  P  R IAMVFQ+YALYPHMTVY+NMAFG++L    + E   R+  AA
Sbjct: 59  TLSINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAA 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           ++L +   L+R P+ LSGGQRQRVA+GRAIVR+P+VFL DEPLSNLDA LRV  R EI +
Sbjct: 119 EMLQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAR 178

Query: 181 LHQRLQ-TTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSP 239
           LHQ ++ TT+IYVTHDQ EAMT+ DRI V+RDG ++Q  TP  +Y +P ++FVAGFIGSP
Sbjct: 179 LHQSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSP 238

Query: 240 AMNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299
            MNF+ G   +      F A ++ LR                    L + PE  H     
Sbjct: 239 KMNFLTGPHAEP-----FGAHTVGLRSEH-----------------LAIVPERGH----- 271

Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSIG-PNTIVARVNPRHVYHVGSSVKLAIDLNKI 358
                      QV   E +GS+ Y++  +G    +V R +       G ++ ++   + +
Sbjct: 272 --------WSGQVVHTEILGSDTYVYIDLGLEEPLVVRESGVSARKPGEALSISPTGDHV 323

Query: 359 HIFD 362
           H FD
Sbjct: 324 HRFD 327


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: 384
Number of extensions: 18
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: 333
Length adjustment: 29
Effective length of query: 355
Effective length of database: 304
Effective search space:   107920
Effective search space used:   107920
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 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