GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Marinobacter adhaerens HP15

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Marino:GFF2209
          Length = 366

 Score =  212 bits (540), Expect = 1e-59
 Identities = 131/357 (36%), Positives = 208/357 (58%), Gaps = 17/357 (4%)

Query: 1   MATLELRNVNKTYG--PGLPD--TLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLET 56
           MA ++L+++  +Y   P  PD   ++ ++     G    L+GPSGCGKST++N I+GL  
Sbjct: 1   MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ 60

Query: 57  ISGGAILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEV 116
            S G +L D   ++ +SP+DR+IA VFQ   +Y +M+V DN+AF LK  K+P ++I   V
Sbjct: 61  PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV 120

Query: 117 ARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRP-KIYLFDEPLSNLDAKLRVEMR 175
             ++++L+IE  L +K   L+  ++Q+V+MGR L R      LFDEPL+ +D +L+ ++R
Sbjct: 121 HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR 180

Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235
            ++K +H++   T VYVTHDQ+EA T  DK+AVM  G I QFGTP +++  P + FV  F
Sbjct: 181 RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF 240

Query: 236 IGSPPMNFIPLRLQRKD---GRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQII 292
           IGSP MN I ++   +    G  +  L+S Q        +Q        + +GIRPE + 
Sbjct: 241 IGSPGMNLIEVQRCPRGVCFGSTVVSLESWQVDV-----LQRT--RSTNIKIGIRPEFVE 293

Query: 293 LANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQF 349
           +++  ++   T  AEV   E  G   +V V L+  K+  R + + A ++G  + L F
Sbjct: 294 VSSVASD--DTFEAEVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSF 348


Lambda     K      H
   0.319    0.138    0.393 

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: 319
Number of extensions: 17
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: 386
Length of database: 366
Length adjustment: 30
Effective length of query: 356
Effective length of database: 336
Effective search space:   119616
Effective search space used:   119616
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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