GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2991
          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.

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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