GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Pseudomonas stutzeri RCH2

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  333 bits (854), Expect = 5e-96
 Identities = 186/366 (50%), Positives = 235/366 (64%), Gaps = 18/366 (4%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           MA V L  I K+Y G   P  +  +LDI+D EF VFVGPSGCGK+T LR+IAGLEDIT G
Sbjct: 1   MASVTLRDICKSYDGT--PITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58

Query: 61  NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120
           +L I ++RVND+PPKDR + MVFQ+YALYPHMTV +NMAFGLKL  V K EI RRV+  A
Sbjct: 59  DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118

Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180
           +IL +  LL+RKPK LSGGQRQRVA+GR +VREP+VFL DEPLSNLDA LRVQMR EI +
Sbjct: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178

Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240
           LHQR+++T+IYVTHDQ EAMT+ D+IVV+  G I Q   P  +Y  PKN FVAGF+GSP 
Sbjct: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238

Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAI---GKPVVLGVRPEDLHDEE 297
           MNF+    +           ++++ LP G    L   G+    G P+ LG+RP     E 
Sbjct: 239 MNFVEVRAISAS------PETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRP-----EH 287

Query: 298 VFMTTYPDSVLQMQVEVVEHMG--SEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDL 355
             M    D     Q+ V E +G  + +YL      + I   V+       G +    +  
Sbjct: 288 FVMPDEADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKA 347

Query: 356 NKIHIF 361
           +K H+F
Sbjct: 348 DKCHLF 353


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: 442
Number of extensions: 15
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: 371
Length adjustment: 30
Effective length of query: 354
Effective length of database: 341
Effective search space:   120714
Effective search space used:   120714
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: 50 (23.9 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