GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Brucella inopinata BO1

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_008509836.1 BIBO1_RS16200 ABC transporter ATP-binding protein

Query= reanno::psRCH2:GFF857
         (371 letters)



>NCBI__GCF_000182725.1:WP_008509836.1
          Length = 333

 Score =  329 bits (843), Expect = 8e-95
 Identities = 185/361 (51%), Positives = 231/361 (63%), Gaps = 31/361 (8%)

Query: 1   MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60
           MA + LRD+ KS+    + + +D+DI  GEF+VFVGPSGCGKSTLLRLIAGLE+ITSG L
Sbjct: 1   MAELQLRDVRKSFGSFEVIKGVDMDIRPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60

Query: 61  LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120
            I+   VN+  P  R + MVFQSYALYPHMTV ENMAFG++LAS  ++E K R+ A AE+
Sbjct: 61  SINGAVVNNFNPSRRGIAMVFQSYALYPHMTVYENMAFGMQLASKSRQECKARIHAAAEM 120

Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180
           LQL   LER P+ LSGGQRQRVAIGR +VR+PKVFLFDEPLSNLDA LRV  R+EIARLH
Sbjct: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIARLH 180

Query: 181 QRIR-STMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239
           Q +  +TMIYVTHDQVEAMTLAD+I VL  G + Q+G PL LY  P + FVAGF+GSP+M
Sbjct: 181 QSMEDTTMIYVTHDQVEAMTLADRICVLRDGRVEQIGTPLELYEKPNSLFVAGFIGSPKM 240

Query: 240 NFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHF-VMPDEADFTF 298
           NF                          + G    P    T+G+R EH  ++P+   ++ 
Sbjct: 241 NF--------------------------LTGPHAEPFGAHTVGLRSEHLAIVPERGHWS- 273

Query: 299 HGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGE 358
            GQ+   E LG    +Y+ L  L++ + +   G      GE  +     D  H F E G 
Sbjct: 274 -GQVVHTEILGSDTYVYIDL-GLEEPLVVRESGVSARKPGEALSISPTGDHVHRFDEKGR 331

Query: 359 A 359
           A
Sbjct: 332 A 332


Lambda     K      H
   0.322    0.139    0.405 

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: 337
Number of extensions: 20
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: 371
Length of database: 333
Length adjustment: 29
Effective length of query: 342
Effective length of database: 304
Effective search space:   103968
Effective search space used:   103968
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 (21.9 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