GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Streptomyces kebangsaanensis SUK12

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein

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



>NCBI__GCF_001906585.1:WP_073948994.1
          Length = 462

 Score =  238 bits (607), Expect = 3e-67
 Identities = 162/482 (33%), Positives = 246/482 (51%), Gaps = 36/482 (7%)

Query: 9   YINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRA 68
           YI+G           EV NPA  QV   V   +  DVD+AV AA+AA P W+ TPP  RA
Sbjct: 8   YIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAERA 67

Query: 69  RVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQ 128
             +    ++L A KDE+AE +T E G     +Q   A          G+P  + G Y + 
Sbjct: 68  ARLTALRDVLVARKDEIAETVTAELGSPLAFSQAVHA----------GVPIAVAGSYADL 117

Query: 129 VST-----GIDNWTT-RQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPS 182
            +T      + N T   +P+GVV  ITP+N+P+   +     A+AAG + VLKP+   P 
Sbjct: 118 AATYAFEEKVGNSTVHHEPVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPL 177

Query: 183 ASLMMADLLKQAGLPDGVFNVVQG-DKDSVEALIDHPDVKALSFVGSTPIANLIYERGAR 241
            + + A+   +AG+P GV N+V G    + +AL +HPDV  +SF GST +   I      
Sbjct: 178 TAQLFAEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGATAGA 237

Query: 242 SGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVP 301
           + KR+    G K+  V++P A+L +AV+  +     ++G+ C A +  ++  D  D+ V 
Sbjct: 238 AVKRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVE 297

Query: 302 RLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTG 361
             A  A         +    +GP+V ++   R+ GYIEKG+AEGA +V  G +       
Sbjct: 298 LAATAA--------AKYGDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPE------- 342

Query: 362 EGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCF 421
             C  G+++  T+F  VTP+MT+ +EEIFGPVL+ +R  D   A+++ N   +G   + +
Sbjct: 343 APCEKGYFVSPTVFADVTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVW 402

Query: 422 TESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQK 481
               + A  F RR+  G V IN     P+A   FGG+K+S  G     G  G+  Y + K
Sbjct: 403 AADETEAVAFARRMDTGQVDINGGRFNPLA--PFGGYKQSGVG--RELGAHGLTEYLQTK 458

Query: 482 SI 483
           S+
Sbjct: 459 SL 460


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: 552
Number of extensions: 22
Number of successful extensions: 6
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: 462
Length adjustment: 34
Effective length of query: 469
Effective length of database: 428
Effective search space:   200732
Effective search space used:   200732
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 24 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