GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Phaeacidiphilus oryzae TH49

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

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



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  296 bits (759), Expect = 5e-85
 Identities = 172/363 (47%), Positives = 225/363 (61%), Gaps = 14/363 (3%)

Query: 1   MASVTLRDICKSYDG--TPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58
           MA+VT     + Y G   P    +DL+I DGEF+V VGPSGCGKST LR++AGLED+ +G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 59  DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118
            + I  + V  LPPKDR + MVFQ+YALYPHMTVA+NM F LK+A V+K EI+ +VE  A
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178
           +IL L + L+RKPK LSGGQRQRVA+GR +VREP+VFL DEPLSNLDA LRV  R +IA 
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238
           L +R+  T +YVTHDQVEAMT+ D++ VL  G + QV  P ++Y  P N FVAGF+GSP 
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 239 MNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGD-PLTLGIRPEHFVMPDEA--- 294
           MN VEV       +       S   ++    G A + GD  +T+G+RPEH  +       
Sbjct: 241 MNLVEVPITDGGVKFG----ESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGG 296

Query: 295 --DFTFHGQITVAERLGQYNLLYLTLERLQDVITLC--VDGNLRVTEGETFAAGLKADKC 350
             D      + V E LG    +Y + +   + I L   V G     +G+      +A + 
Sbjct: 297 GEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGET 356

Query: 351 HLF 353
           H+F
Sbjct: 357 HVF 359


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: 403
Number of extensions: 19
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: 369
Length adjustment: 30
Effective length of query: 341
Effective length of database: 339
Effective search space:   115599
Effective search space used:   115599
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 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