GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Klebsiella michiganensis M5al

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BWI76_RS02840 BWI76_RS02840 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= metacyc::MONOMER-15203
         (503 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS02840 BWI76_RS02840
           methylmalonate-semialdehyde dehydrogenase (CoA
           acylating)
          Length = 503

 Score =  447 bits (1150), Expect = e-130
 Identities = 220/496 (44%), Positives = 322/496 (64%), Gaps = 5/496 (1%)

Query: 2   TIKRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSD 61
           T+ R++++++G       + + +V NP+TG+V  Q    ++ +V  AVAAA+ AFPAWSD
Sbjct: 3   TVPRLKYFVDGQWRVSQTERYMDVYNPSTGEVMAQAPCCTEQEVLDAVAAARKAFPAWSD 62

Query: 62  TPPIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLL 121
           TP I+R+++MF+  ELL  H+D L E + +E+GK + DAQG+V +  +  E AC IP L+
Sbjct: 63  TPAIKRSQIMFRVRELLIQHQDRLTELVAKENGKAWGDAQGDVLKAKEGTELACSIPTLM 122

Query: 122 KGDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPM-WMFPLAIAAGNSFVLKPSPLD 180
            G+     S GID    R+P+GV AGI PFNFP M+PM WM PL +A+GN+ V+K + + 
Sbjct: 123 AGENLMDASAGIDTNLYREPIGVFAGIVPFNFPAMIPMGWMAPLCVASGNTMVIKAASMT 182

Query: 181 PSASLMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGA 240
           P   + +  L ++AG+PDGV NVV   ++  + L+ HPDV  +SFVGST +   +Y + A
Sbjct: 183 PMTCMEITKLYQEAGVPDGVINVVTCSRNEADILLTHPDVNGVSFVGSTSVGLHVYSKAA 242

Query: 241 RSGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIV 300
             GKR+QAL  AKNH +V+ DA +++    +I AA+G AGERCMA+ V V+  ++ADK++
Sbjct: 243 AHGKRVQALCEAKNHALVLADAPINRTAAGIINAAFGCAGERCMALPVVVVQEEIADKLI 302

Query: 301 PRLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVT 360
             + E+A+ LKI  G   D +MGP+++    + + G+I KG+ EGA++V+DGRD    + 
Sbjct: 303 AAVVEKAKQLKIGPGYLRDTDMGPVISKDHKRSVIGWINKGIEEGAKLVLDGRD----IK 358

Query: 361 GEGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSC 420
             G  +GF++G T+ D VT EM++  +EIFGPVL   RV      +QL+N++ F NG   
Sbjct: 359 VPGQENGFYVGPTILDRVTEEMSVGTQEIFGPVLCFKRVKTFEEGLQLMNNNPFANGSVI 418

Query: 421 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQ 480
           FT+SG  AREF +R   GMVGINV IPVP+    F G K+S FGD H  G++GVRFYT+ 
Sbjct: 419 FTQSGYYAREFQKRTHGGMVGINVGIPVPVGVFPFSGHKQSFFGDLHCLGKDGVRFYTES 478

Query: 481 KSIMQRWSDSIDAGAE 496
           K +  RW D  +A  E
Sbjct: 479 KCVTSRWFDEEEAKRE 494


Lambda     K      H
   0.319    0.136    0.406 

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: 715
Number of extensions: 23
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: 503
Length of database: 503
Length adjustment: 34
Effective length of query: 469
Effective length of database: 469
Effective search space:   219961
Effective search space used:   219961
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