GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>FitnessBrowser__Burk376:H281DRAFT_04155
          Length = 369

 Score =  376 bits (965), Expect = e-109
 Identities = 192/364 (52%), Positives = 256/364 (70%), Gaps = 2/364 (0%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60
           MA++ ++N++K ++   +++ I+L++ D EFVVFVGPSGCGKSTL+R+IAGLE++SGG +
Sbjct: 1   MASVTLRNIRKAYDDTEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60

Query: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120
            ++G  + +V PAKR +AMVFQ+YALYPHM++  NM+F L LAG  K E++  V  AA+I
Sbjct: 61  TINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120

Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180
           L +  +L+RKPKQLSGGQRQRVAIGRAI R PK+FLFDEPLSNLDAALRV+MRLE  RLH
Sbjct: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180

Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240
            EL+ TMIYVTHDQVEAMT+ADK+VVL+ G +EQVGSP  LYH PAN FVAGF+G+PKM 
Sbjct: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240

Query: 241 FLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQV 300
           F++G +  V   G  V+ + G    + +    +  G  VT+GIRPEHL +    D     
Sbjct: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPGAVKQGDKVTVGIRPEHLHVGMTDDGVSAR 300

Query: 301 TADVSERLGSDTFCHVRTA-SGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDADGVAL 359
           T  V E LG   + +  ++ + + L  R+        GET  L    +HCHLFD++G A 
Sbjct: 301 TMAV-ESLGDAAYLYAESSVAPDGLIARIPPLERHAKGETQKLGATPEHCHLFDSEGKAF 359

Query: 360 TRPL 363
            R +
Sbjct: 360 QRKI 363


Lambda     K      H
   0.320    0.137    0.389 

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: 423
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: 367
Length of database: 369
Length adjustment: 30
Effective length of query: 337
Effective length of database: 339
Effective search space:   114243
Effective search space used:   114243
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 17 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