GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mt2d in Klebsiella michiganensis M5al

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BWI76_RS15490 BWI76_RS15490 mannitol dehydrogenase family protein

Query= BRENDA::O08355
         (493 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS15490 BWI76_RS15490 mannitol
           dehydrogenase family protein
          Length = 487

 Score =  339 bits (870), Expect = 1e-97
 Identities = 190/479 (39%), Positives = 268/479 (55%), Gaps = 8/479 (1%)

Query: 11  LAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDR 70
           L     LPAY        I H+G G FHRAHQA Y D L  T  G DW    V L   ++
Sbjct: 6   LTANATLPAYDRNRLIPRIVHLGFGAFHRAHQAVYADILA-TEHGSDWGYTEVNLIGGEQ 64

Query: 71  KARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAE-DSAQALIDKLASPEIRIVSL 129
           +  D L  QD L+T+ E+   D    RV+G +   + A+ D  ++++ K+  P++ IVSL
Sbjct: 65  QIAD-LQKQDLLYTVAEMS-ADAWTARVVGVVKQAMHAQVDGLESVLAKMCEPQVAIVSL 122

Query: 130 TITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSC 189
           TITE GYC   ++GE     P I  DL +P  PK+  G +  AL +R+AAG+PAF+VMSC
Sbjct: 123 TITEKGYCHSPASGELQLDHPLIAADLQNPRQPKSAPGVVVEALARRKAAGLPAFSVMSC 182

Query: 190 DNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHG 249
           DN+P NG V R  + A+A   +A+L +WI  +V+FP+ MVDRI P  +     ++    G
Sbjct: 183 DNMPENGHVMRNVICAYARAVDADLAEWITRNVTFPSTMVDRIVPAVTADTLDKIAQLTG 242

Query: 250 IDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYL 309
           + D   V CEPF QWV+ED FV GRP WEK G +   DV P+EEMK+ +LNGSH  L YL
Sbjct: 243 VRDPAAVACEPFRQWVIEDNFVAGRPQWEKAGAELVSDVLPFEEMKLRMLNGSHSFLAYL 302

Query: 310 GFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIAD 369
           G+L GY+ +++ M D  +       M  +  P L+ V G+DL  Y   L++R+SN A+  
Sbjct: 303 GYLAGYQHINDCMQDANYRRAAHTLMLAEQAPTLS-VKGVDLARYAGLLIERYSNPALKH 361

Query: 370 QLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPDP 429
           +  ++  DGS K P+  + +I   +ADG +    A+ VA W  Y+ GVD+ G +  I DP
Sbjct: 362 RTWQIAMDGSQKLPQRMLDSIRWHLADGGDFPLLAMGVAGWMRYVSGVDDQGQAIEISDP 421

Query: 430 RAEFCQGLVSDDALISQR---LLAVEEIFGTAIPNSPEFVAAFERCYGSLRDNGVTTTL 485
                   V +     +R   LL +E IFG ++P    FV A  R Y SL+ +G   T+
Sbjct: 422 MLPVITQTVQNSEDGEERVRALLGIEAIFGLSLPKESRFVNAVVRAYLSLQAHGAKATV 480


Lambda     K      H
   0.321    0.137    0.414 

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: 602
Number of extensions: 31
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: 493
Length of database: 487
Length adjustment: 34
Effective length of query: 459
Effective length of database: 453
Effective search space:   207927
Effective search space used:   207927
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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