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 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