GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dddA in Klebsiella michiganensis M5al

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate BWI76_RS07610 BWI76_RS07610 choline dehydrogenase

Query= metacyc::MONOMER-15202
         (579 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07610 BWI76_RS07610 choline
           dehydrogenase
          Length = 554

 Score =  327 bits (838), Expect = 8e-94
 Identities = 215/546 (39%), Positives = 288/546 (52%), Gaps = 29/546 (5%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHW---IHIPVGYLYCINNPRTD 92
           FDYI++GAG+AG +LA RL+ DP   VLL+EAGG D Y +     +P    + +   R +
Sbjct: 3   FDYIIIGAGSAGNVLATRLTEDPDTTVLLLEAGGPD-YRFDFRTQMPAALAFPLQGRRYN 61

Query: 93  WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152
           W + TEP+P +N R +   RGK LGG S INGM Y+RG A D D WA   G + W + +C
Sbjct: 62  WAYETEPEPHMNHRRMECGRGKGLGGSSLINGMCYIRGNAMDLDNWASAPGLEHWSYLDC 121

Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW---QVLADFATAAVEAGV 209
           LP       +YR  E  D   + Y    HGG+  +     K     +      A V+AG 
Sbjct: 122 LP-------YYRKAETRDIGANDY----HGGDGPVSVTTPKQGNNPLFHAMIEAGVQAGY 170

Query: 210 PRTRDFNRGDNEGVDAFEVNQR-SGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASG 268
           PRT D N    EG    +      G R + ++ +L     R NLT+        + FA  
Sbjct: 171 PRTDDLNGYQQEGFGPMDRTVTPQGRRASTARGYLDQARARPNLTIRTHALTDHIIFAG- 229

Query: 269 EGSEPRCCGVTVERAGKKVVT--TARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326
                R  GV          +  TA  EV+L AGAI SPQ+LQ SG+G   LL +  I +
Sbjct: 230 ----KRAVGVEWLEGDSTAPSKATANKEVLLCAGAIASPQILQRSGVGSPELLRQFDISL 285

Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQ 386
           V  LPGVGENLQDHL++   Y+ K   +L   A     + KIG E++   +G  +    +
Sbjct: 286 VHALPGVGENLQDHLEMYLQYECKEPVSLYP-ALQWWNQPKIGAEWLFGGTGIGASNQFE 344

Query: 387 LCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNP 446
              F RS + +  PN++YH  P+++   G            V ++   SRG VR+KS +P
Sbjct: 345 AGGFIRSREAFAWPNIQYHFLPVAINYNGSNAVKEHGFQCHVGSMRSPSRGHVRLKSRDP 404

Query: 447 RQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLA 506
            Q PAI  NY+S E+D Q   D++R+TR I SQPA   Y   E  PG++ QSD +L    
Sbjct: 405 HQHPAILFNYMSHEQDWQEFRDAIRITREIMSQPALDNYRGREISPGIECQSDAELDEFV 464

Query: 507 GDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566
            +   T FHP GT KMG D+  MAVVD   RV G+ GLRVVDASIMP I +GN N+ T+M
Sbjct: 465 RNHAETAFHPCGTCKMGYDE--MAVVDGEGRVHGLEGLRVVDASIMPQIITGNLNATTIM 522

Query: 567 IAEKAA 572
           I EK A
Sbjct: 523 IGEKMA 528


Lambda     K      H
   0.318    0.135    0.418 

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: 982
Number of extensions: 42
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: 579
Length of database: 554
Length adjustment: 36
Effective length of query: 543
Effective length of database: 518
Effective search space:   281274
Effective search space used:   281274
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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