GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Psychromonas ingrahamii 37

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_011770383.1 PING_RS10725 choline dehydrogenase

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



>NCBI__GCF_000015285.1:WP_011770383.1
          Length = 562

 Score =  354 bits (909), Expect = e-102
 Identities = 214/542 (39%), Positives = 305/542 (56%), Gaps = 19/542 (3%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DYI+VGAG+AGC+LANRLS DP N++LL+E GG D   +I +P      +N+ +  W+F
Sbjct: 6   YDYIIVGAGSAGCVLANRLSEDPENQILLLETGGSDKSIFIQMPTALSIPMNSKKYAWQF 65

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            T+ +P L+ R +  PRGK LGG SSINGM+Y+RG ARD+D W + +G   W + +CLP 
Sbjct: 66  ETQAEPFLDNRRMHCPRGKVLGGSSSINGMVYVRGHARDFDEW-QASGAKDWDYAHCLPY 124

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEK-QRLKWQVLADFATAAVEAGVPRTRD 214
           F + E       GG+       + G  G   +     +K  +   F  A V+AG   T+D
Sbjct: 125 FKKAE---TWSFGGN------DYRGDTGPLAVNNGNNMKNPLYQAFVDAGVDAGYLATKD 175

Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274
           +N    EG     +  ++G RW+ + A+LR   +R NLTV     V K+     EG   +
Sbjct: 176 YNAEQQEGFGPMHMTVKNGVRWSTANAYLRPAMKRNNLTVVTHALVHKVLL---EGK--K 230

Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334
             GV  E  G+   T    EV+L AG+IGSP +LQLSGIG    LA+  I    +LPGVG
Sbjct: 231 AVGVRYEVKGQLTDTRCNKEVLLCAGSIGSPHILQLSGIGEADTLAQAGIEQHHELPGVG 290

Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394
           +NLQDHL+    +K     +LN     L  K  IG+ +IL +SG  +    + C F RS 
Sbjct: 291 KNLQDHLEFYFQFKCLKPISLNGQLGPL-NKLLIGVRWILNKSGLGATNHFESCGFIRSK 349

Query: 395 KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAISP 454
              E P+L+YH  P ++   G+           V +  P SRG V+I S +   AP I  
Sbjct: 350 NSLEWPDLQYHFLPAAMRYDGKEAFAGHGFQVHVGHNKPKSRGAVKIVSKDAHIAPQIQF 409

Query: 455 NYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTTIF 514
           NYLS ++D +     +R+TR I +QP   +Y  EE +PG+  QSD+++ +       + +
Sbjct: 410 NYLSHQDDIEAFRACVRLTREIINQPGLDEYRGEEIQPGLAIQSDQEIDQFVRSSVESAY 469

Query: 515 HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAAGW 574
           HP  + KMG  +D M+VV+S  +V G+  LRVVD+SI PTI +GN NSPT+M+AE+AA  
Sbjct: 470 HPSCSCKMG--EDAMSVVNSDTKVHGIEALRVVDSSIFPTIPNGNLNSPTIMVAERAADI 527

Query: 575 IL 576
           IL
Sbjct: 528 IL 529


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: 888
Number of extensions: 48
Number of successful extensions: 5
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: 562
Length adjustment: 36
Effective length of query: 543
Effective length of database: 526
Effective search space:   285618
Effective search space used:   285618
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 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