Alignments for a candidate for dddA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_068167937.1 HTA01S_RS06370 choline dehydrogenase

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



>NCBI__GCF_001592305.1:WP_068167937.1
          Length = 556

 Score =  402 bits (1032), Expect = e-116
 Identities = 239/544 (43%), Positives = 318/544 (58%), Gaps = 16/544 (2%)

Query: 30  TNNTHAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNP 89
           T    AFDYI++GAG+AG  LA RL  D   ++L+IEAG  D+  +IH+P  + Y + NP
Sbjct: 2   TKPAAAFDYIIIGAGSAGSTLAYRLGEDLDVKILVIEAGPMDHNLFIHMPSAFAYPMANP 61

Query: 90  RTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRW 149
           R  W+F  E DPG+N R +  PRGKT+GG SSINGM+Y+RG A DY+GWAE  G   WR+
Sbjct: 62  RYSWQFEAEADPGMNNRRIHCPRGKTIGGSSSINGMVYIRGHAEDYNGWAEQFGLPEWRY 121

Query: 150 DNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGV 209
            NCLP F + E     ++GG    DHY+  G  G  ++   R +  +   F  A  EAG 
Sbjct: 122 ANCLPYFRKSETR---EQGG----DHYR--GSDGPLKVSTGRCENPLYKAFIEAGQEAGY 172

Query: 210 PRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGE 269
             T D N    EG    ++    G RW+ + A+LR   +RGN+T+   T V ++ F   E
Sbjct: 173 GYTADMNGHRQEGFGPMDMTVHKGRRWSTAMAYLRPALKRGNVTLHTGTAVSRILF---E 229

Query: 270 GSE-PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVA 328
           G + PR  GV VE+ G+KVV  A+ EV+LSAGAI SPQLLQLSG+G   LL    IPVVA
Sbjct: 230 GKDLPRAVGVEVEQGGQKVVYRAQREVILSAGAIQSPQLLQLSGVGHPDLLRPLGIPVVA 289

Query: 329 DLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLC 388
              GVGENLQDHL+    Y  K   TL + A   +    IG +++L R+G  +    +  
Sbjct: 290 ARAGVGENLQDHLETYVQYACKEPITLYS-ATKPLAMGAIGAQWLLTRTGLGATNHFESG 348

Query: 389 IFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448
            F RS     HP+L+YH  P+++   G          A V  +  TSRG VRI+S + R 
Sbjct: 349 GFIRSDAGVRHPDLQYHFLPMAVRYDGSATVAGHGFQAHVGPMRSTSRGHVRIRSASHRD 408

Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGD 508
           AP I  NY+ST++DR+    ++R+TR + +Q AF ++  EE  P  Q QSD ++     +
Sbjct: 409 APEIRFNYMSTDQDRKEFRAAIRLTREVFAQNAFHRFRGEELSPTAQVQSDAEIDEHIRN 468

Query: 509 IGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIA 568
              T +HP  + +MG DD  MAVVD   RV GV  LRVVDASIMP I SGN N PT+M+A
Sbjct: 469 QAETAYHPSCSCRMGHDD--MAVVDGEGRVHGVQALRVVDASIMPLIVSGNLNVPTIMMA 526

Query: 569 EKAA 572
           EK A
Sbjct: 527 EKIA 530


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: 889
Number of extensions: 43
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: 556
Length adjustment: 36
Effective length of query: 543
Effective length of database: 520
Effective search space:   282360
Effective search space used:   282360
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources