GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Psychromonas ossibalaenae JAMM 0738

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_019615884.1 G327_RS0116375 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_024820
         (891 letters)



>NCBI__GCF_000381745.1:WP_019615884.1
          Length = 879

 Score = 1227 bits (3174), Expect = 0.0
 Identities = 607/883 (68%), Positives = 728/883 (82%), Gaps = 4/883 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M V+ VA+L AL+ RVK AQ EYA+F+QE+VD+IFR AAL  +  RI LAKMAV E+GMG
Sbjct: 1   MTVSTVADLEALIARVKLAQAEYATFSQEKVDEIFRVAALKVSTHRIELAKMAVKETGMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           I+EDKVIKNHFASE+IYN++ D KT G LS +++  T+T+AEP+GIIC IVPTTNPTSTA
Sbjct: 61  IIEDKVIKNHFASEFIYNSFADTKTVGELSRNESLNTVTLAEPMGIICAIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFK+L++LKT N  I +PHPRAK+ TN AA IVL AAI AGAPKD+IGWID PS+EL+N 
Sbjct: 121 IFKTLMALKTGNGCIVAPHPRAKECTNYAAKIVLDAAIEAGAPKDIIGWIDIPSLELTNT 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           +M H D  +ILATGGPGMVKAAYSSG PAIGVGAGNTPVVIDE+ADIKRAV+S+LMSKTF
Sbjct: 181 IMKHDDTAIILATGGPGMVKAAYSSGNPAIGVGAGNTPVVIDESADIKRAVSSILMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNG+ICASEQ+ +VV+S YD  + R   +GG++L   + K V D +  +GALNA IVGQ 
Sbjct: 241 DNGMICASEQAAIVVESKYDEFKARLEEYGGFMLNEADTKKVADTMFIDGALNAKIVGQS 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A+ IAELAG  VP +TK+L+GE   V E   FAHEKLSPTL +++AK++EDAV +A+ ++
Sbjct: 301 AFTIAELAGVKVPTSTKVLVGEGLEVKEENMFAHEKLSPTLGLFKAKNYEDAVRQAQIVL 360

Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420
            +GG+GHT+ LYTDQD    RV  FG  MK  RI+IN+P S GGIGD+YNF  APSLTLG
Sbjct: 361 DIGGVGHTAALYTDQDANSERVDAFGLAMKACRIVINSPTSHGGIGDIYNFGFAPSLTLG 420

Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480
           CG+  GN++SENVGP+HLIN KT+AKRAENMLWHKLPKSIYFRRGSLPIA+ ++  +G +
Sbjct: 421 CGTHSGNAVSENVGPQHLINTKTIAKRAENMLWHKLPKSIYFRRGSLPIAMTDL--EGKQ 478

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RA+IVTD FLF NGY D++ S+L++ G+  EVF EVEADPTLSI++KGA   N+F PDVI
Sbjct: 479 RAMIVTDGFLFANGYIDELRSILESKGMMVEVFHEVEADPTLSIIQKGAAACNAFNPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           +A+GGGSPMDAAKIMWV+YEHP T FE+LA+RFMDIRKRIYKFPKMGVKA+++ +TTTSG
Sbjct: 539 LAVGGGSPMDAAKIMWVLYEHPATDFEDLAMRFMDIRKRIYKFPKMGVKAELVCITTTSG 598

Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660
           TGSEVTPFAVVTDD TG+KYPLADY LTP+MA+VDANLVMDMPKSLCAFGG DAVTHA+E
Sbjct: 599 TGSEVTPFAVVTDDKTGKKYPLADYELTPNMAVVDANLVMDMPKSLCAFGGYDAVTHAVE 658

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVS+LA+E+SDGQALQ+LKLLKEYLP+SYH G  + VARE+VH+AATIAGIAFAN+FLG
Sbjct: 659 AYVSMLANEYSDGQALQSLKLLKEYLPSSYHNGKNDAVAREKVHNAATIAGIAFANSFLG 718

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           VCHSMAHK+G++FHIPHGLANALL+ N IR+NA + PTKQ  FSQYDRP+AR RYAEIA 
Sbjct: 719 VCHSMAHKIGNEFHIPHGLANALLLTNTIRFNATNKPTKQGTFSQYDRPKARARYAEIAV 778

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HLG       T  KI  LL WL+ LK EL IP SI+ AGV EADFLA +D L+E AFDDQ
Sbjct: 779 HLGFYE--GNTEDKINALLTWLDELKVELNIPLSIQAAGVNEADFLAALDDLAEQAFDDQ 836

Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKA 883
           CTGANPRYPLISELK++LL +YYG+DYV+   A   E    +A
Sbjct: 837 CTGANPRYPLISELKEVLLASYYGKDYVDVVDAPAVEETEEEA 879


Lambda     K      H
   0.317    0.132    0.378 

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: 1852
Number of extensions: 69
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: 891
Length of database: 879
Length adjustment: 43
Effective length of query: 848
Effective length of database: 836
Effective search space:   708928
Effective search space used:   708928
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: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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