GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS07610
          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:

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