GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Amantichitinum ursilacus IGB-41

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_053936073.1 WG78_RS01880 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_024820
         (891 letters)



>NCBI__GCF_001294205.1:WP_053936073.1
          Length = 888

 Score = 1362 bits (3525), Expect = 0.0
 Identities = 683/891 (76%), Positives = 774/891 (86%), Gaps = 4/891 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           MAVTNV EL+ALV RVKKAQ+++A+F+QEQVD+IFR AALAAADARIPLA+MAV E+GMG
Sbjct: 1   MAVTNVQELDALVARVKKAQQQFATFSQEQVDEIFRCAALAAADARIPLARMAVTETGMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           ++EDKVIKNHFASEYIYNAYKDEKTCGVL  D  FGT+TIAEPIGIICGIVPTTNPTSTA
Sbjct: 61  VLEDKVIKNHFASEYIYNAYKDEKTCGVLEVDALFGTMTIAEPIGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFK+LISLKTRN IIFSPHPRA+ +T +AA IVL+AA+AAGAPKD+IGWID PSVELSNA
Sbjct: 121 IFKALISLKTRNGIIFSPHPRARKSTCEAARIVLEAAVAAGAPKDIIGWIDAPSVELSNA 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           LMHH D NLILATGGPGMVKAAYSSGKPAIGVGAGNTPVV+DETADIKR VAS+LMSKTF
Sbjct: 181 LMHHKDTNLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVVDETADIKRMVASILMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGV+CASEQSV++VD VY+  ++RF   GGY+L  KE +AV+ VIL NG LNA IVGQ 
Sbjct: 241 DNGVVCASEQSVIIVDEVYEQAKDRFVRAGGYVLNKKETEAVRKVILVNGGLNANIVGQS 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A +IAE+AG +VP  TK+LIGEV  V + E FAHEKLSPTLAMYRAKDF DAVEKA  LV
Sbjct: 301 AARIAEMAGITVPSYTKVLIGEVASVGDEEAFAHEKLSPTLAMYRAKDFYDAVEKAVALV 360

Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420
           A+GGIGHTS LYT+QD Q  R++YFG KMKTARILINTP+SQGGIGDLYNFKLAPSLTLG
Sbjct: 361 ALGGIGHTSALYTNQDMQDERIAYFGDKMKTARILINTPSSQGGIGDLYNFKLAPSLTLG 420

Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480
           CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPK+IYFRRG LP AL ++  +G K
Sbjct: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKNIYFRRGCLPFALRDL--EGKK 478

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RA IVT  FLFNNGY D+   +LK  G+E EVFFEVEADPTL +VRKG    N FKPDVI
Sbjct: 479 RASIVTGSFLFNNGYCDETIRILKQMGMEVEVFFEVEADPTLEVVRKGVHALNVFKPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           IALGGGSPMDAAKIMWVMYEHPE HFE+LALRFMDIRKRIYKFPKMG+KA+++A+ TTSG
Sbjct: 539 IALGGGSPMDAAKIMWVMYEHPEVHFEDLALRFMDIRKRIYKFPKMGIKAELVAIPTTSG 598

Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660
           TGSEVTPFAVVTD+ TG KYP+ADY LTP+MAI+DA+LVMDMPKSL AFGG+DAVTHA+E
Sbjct: 599 TGSEVTPFAVVTDEKTGTKYPIADYELTPNMAIIDADLVMDMPKSLTAFGGIDAVTHALE 658

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVSV+A+E+SD QALQAL LLK YLP+SY  G+ +P ARE+VH+AATIAG+AFANAFLG
Sbjct: 659 AYVSVMANEYSDPQALQALTLLKAYLPSSYANGANDPRAREQVHNAATIAGVAFANAFLG 718

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           VCHSMAHKLG++FH+ HGLANALLI NVIRYNA D PTKQTAFSQYDRPQA+ RYA+IA+
Sbjct: 719 VCHSMAHKLGAEFHLAHGLANALLITNVIRYNAVDIPTKQTAFSQYDRPQAKCRYADIAE 778

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HLGL    D    K+E L+AW+  LK  LGIP SI+ AGV EA FL+ +D+++E+AFDDQ
Sbjct: 779 HLGLGGKDD--DEKVEALIAWVNELKNVLGIPASIQAAGVPEALFLSKLDEVAEEAFDDQ 836

Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA 891
           CTGANPRYPLISELKQ+LLD+YYGR YVE     + EA  AKA+  AK +A
Sbjct: 837 CTGANPRYPLISELKQLLLDSYYGRTYVESYEREQVEAVVAKAQAAAKAAA 887


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: 1918
Number of extensions: 59
Number of successful extensions: 4
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: 888
Length adjustment: 43
Effective length of query: 848
Effective length of database: 845
Effective search space:   716560
Effective search space used:   716560
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.

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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