Aligments for a candidate for dddA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for dddA in Phaeobacter inhibens BS107

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF2991 PGA1_c30400 alcohol dehydrogenase AlkJ

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



>lcl|FitnessBrowser__Phaeo:GFF2991 PGA1_c30400 alcohol dehydrogenase
           AlkJ
          Length = 529

 Score =  632 bits (1629), Expect = 0.0
 Identities = 333/544 (61%), Positives = 391/544 (71%), Gaps = 23/544 (4%)

Query: 35  AFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWR 94
           ++DYI+VGAG+AGC+LANRLSA    RVLL+EAGG+DNYHW+HIP+GYLYCINNPRTDW 
Sbjct: 2   SWDYIIVGAGSAGCVLANRLSA-AGQRVLLLEAGGKDNYHWVHIPMGYLYCINNPRTDWM 60

Query: 95  FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154
           +RTE + GLNGR+LIYPRGK LGGCSSINGMLYLRGQA DYDGW +  G   W WD+ LP
Sbjct: 61  YRTEAEAGLNGRALIYPRGKVLGGCSSINGMLYLRGQAADYDGWRQ-RGLTGWGWDDVLP 119

Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214
            F + ED+      G +D      HG GGEWR+E QRL W VL D+  AA E G+P+  D
Sbjct: 120 YFKKSEDYV----DGSSD-----MHGVGGEWRVENQRLHWDVLDDWMQAAAEWGLPKVTD 170

Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274
           FN G+NEGV  F VNQRSGWR N +KAFLR      NL V       ++   +G     R
Sbjct: 171 FNTGNNEGVGYFRVNQRSGWRMNTAKAFLRTATGE-NLKVETGAHTRRILIENG-----R 224

Query: 275 CCGVTVERAGKKVVTTARC--EVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332
             GV   + G   V TAR   EV+LSAGAI SPQ+LQLSG+GP ALL +H I V  D+P 
Sbjct: 225 AVGVEYSQGG--AVKTARTGGEVLLSAGAINSPQILQLSGLGPEALLRDHGIAVQRDMPE 282

Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392
           VG+NLQDHLQ+R  +++KGAKTLNT+ANSLIGKAKI  EY ++RSGPMSMAPSQL  F+R
Sbjct: 283 VGQNLQDHLQLRCAWRLKGAKTLNTLANSLIGKAKIAAEYAMRRSGPMSMAPSQLGAFSR 342

Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452
           S  +   P+LEYHVQPL+LEAFGQPLHDFP +TASVCNL P SRG V I S +P QAP I
Sbjct: 343 SRPDLATPDLEYHVQPLTLEAFGQPLHDFPGLTASVCNLRPESRGEVAITSADPMQAPRI 402

Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTT 512
           +PNYLSTE DRQVA  ++R  R I  Q A  +Y P E KPG       DL + AG IGTT
Sbjct: 403 APNYLSTEGDRQVAVAAIRQARAIMGQEAMQRYAPVEMKPGGGSDEAADLMQAAGAIGTT 462

Query: 513 IFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572
           IFHP  T +MG ++   A VD  LR+RGV GLRVVDAS+MP I SGNTN+PT+MIAEKAA
Sbjct: 463 IFHPTCTLRMGAEE--AAPVDGALRLRGVGGLRVVDASVMPVIPSGNTNAPTIMIAEKAA 520

Query: 573 GWIL 576
             IL
Sbjct: 521 DMIL 524


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: 956
Number of extensions: 35
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: 529
Length adjustment: 36
Effective length of query: 543
Effective length of database: 493
Effective search space:   267699
Effective search space used:   267699
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 preprint 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

GapMind for catabolism of small carbon sources