GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Pseudomonas fluorescens FW300-N1B4

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  316 bits (809), Expect = 8e-91
 Identities = 171/365 (46%), Positives = 236/365 (64%), Gaps = 17/365 (4%)

Query: 3   RVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNL 62
           ++ L+++ K   G     ++D +L+I   EF VFVGPSGCGK+T LR+IAGL+ I  G+L
Sbjct: 3   KLKLDNVNKQLGGMR--ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60

Query: 63  YIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKI 122
            I  RRVND+ P++R + MVFQ+YALYPHM+VY N++FGLKL K  K  +  RV + A+I
Sbjct: 61  LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120

Query: 123 LDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLH 182
           L +  LL RKPK LSGGQRQRVA+GRA+ REP + L DEPLSNLDA LRVQMR EI +LH
Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180

Query: 183 QRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMN 242
            RL +T+IYVTHDQ EAMT+ D+IVV+  G ++Q  +P+ +Y +P + FVAGF+GSP MN
Sbjct: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240

Query: 243 FIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASG--AIGKPVVLGVRPEDLHDEEVFM 300
           F+   +   G+       S+   L  G   +   S   A G P+ LG+RPE +  +    
Sbjct: 241 FLSARLQTPGET------SLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAA-- 292

Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPN-TIVARVNPRHVYHVGSSVKLAIDLNKIH 359
               D    + V  VE++GSE Y+H   G +  ++ R      +  G  V+L +DL+ +H
Sbjct: 293 ----DGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLH 348

Query: 360 IFDAE 364
           +FDA+
Sbjct: 349 LFDAD 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: 411
Number of extensions: 21
Number of successful extensions: 4
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: 381
Length adjustment: 30
Effective length of query: 354
Effective length of database: 351
Effective search space:   124254
Effective search space used:   124254
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