Alignments for a candidate for dddA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Marinobacter adhaerens HP15

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF2712 HP15_2656 glucose-methanol-choline oxidoreductase

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



>FitnessBrowser__Marino:GFF2712
          Length = 556

 Score =  943 bits (2438), Expect = 0.0
 Identities = 452/554 (81%), Positives = 495/554 (89%), Gaps = 4/554 (0%)

Query: 26  MADQTNNT--HAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYL 83
           M+D  N T    FDYI++GAGTAGCLLANRLSA+P NRVLLIEAGGRDNYHWIHIPVGYL
Sbjct: 1   MSDNNNATGHQEFDYIIIGAGTAGCLLANRLSANPENRVLLIEAGGRDNYHWIHIPVGYL 60

Query: 84  YCINNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTG 143
           YCI+NPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLY+RGQARDY  WAE+TG
Sbjct: 61  YCIDNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYIRGQARDYQQWAEITG 120

Query: 144 DDAWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATA 203
           +DAW WDNCLPDFMRHEDHYRLDEGGDADP+H K+HGHGGEWR+E QRLKW+VL DFATA
Sbjct: 121 EDAWNWDNCLPDFMRHEDHYRLDEGGDADPEHRKYHGHGGEWRVEHQRLKWKVLEDFATA 180

Query: 204 AVEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKL 263
            VEAG+PRTRDFNRGDNEGVD FEVNQRSGWRWN SKAFLR  E+R NLT+WHST VL L
Sbjct: 181 CVEAGIPRTRDFNRGDNEGVDYFEVNQRSGWRWNTSKAFLRNAEKRSNLTLWHSTHVLGL 240

Query: 264 DFASGEGSEPRCCGVTVERAG-KKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEH 322
           +     GS PRC GV VER+G   V+  A+ EV+LSAGAIGSPQLLQLSGIGP  LL EH
Sbjct: 241 E-TENAGSGPRCVGVRVERSGGDDVIARAKREVILSAGAIGSPQLLQLSGIGPAHLLKEH 299

Query: 323 AIPVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSM 382
            I VVADLPGVGENLQDHLQIRS+YKVKG  TLNTMANSLIGKA+IGLEY+L RSGPMSM
Sbjct: 300 GIDVVADLPGVGENLQDHLQIRSVYKVKGVTTLNTMANSLIGKARIGLEYLLTRSGPMSM 359

Query: 383 APSQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIK 442
           APSQLC+FTRSS+EY++ N+EYHVQPLSL+AFGQPLH+FPAITASVCNLNPTSRGTVRI+
Sbjct: 360 APSQLCLFTRSSEEYDYANIEYHVQPLSLDAFGQPLHNFPAITASVCNLNPTSRGTVRIR 419

Query: 443 SGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDL 502
           S +P+QAPAISPNYLST EDR+VAADSLRVTR IA QPAF +Y PEEFKPG++YQ+D++L
Sbjct: 420 SNDPKQAPAISPNYLSTPEDRKVAADSLRVTRRIAEQPAFMQYQPEEFKPGLEYQTDDEL 479

Query: 503 ARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNS 562
           A+LAGDIGTTIFHPVGT +MGR DD  AVVD HLRVRGV GLRVVDA +MPTITSGNTNS
Sbjct: 480 AKLAGDIGTTIFHPVGTTRMGRADDEQAVVDPHLRVRGVAGLRVVDAGVMPTITSGNTNS 539

Query: 563 PTLMIAEKAAGWIL 576
           PTLMIAEKAA WIL
Sbjct: 540 PTLMIAEKAARWIL 553


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: 1175
Number of extensions: 36
Number of successful extensions: 3
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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