GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA 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)



>FitnessBrowser__Koxy:BWI76_RS02840
          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:

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