Alignments for a candidate for adh in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Escherichia coli BW25113

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 15361 b1241 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase (NCBI)

Query= CharProtDB::CH_018413
         (862 letters)



>FitnessBrowser__Keio:15361
          Length = 891

 Score =  987 bits (2551), Expect = 0.0
 Identities = 486/862 (56%), Positives = 646/862 (74%), Gaps = 4/862 (0%)

Query: 1   MKVTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMG 60
           M VT V EL+  ++ +K+AQ++++ ++QE VD+IFR AA+AA DARI LAK AV E+GMG
Sbjct: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60

Query: 61  LVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTT 120
           +VEDKVIKNHFA EYIYN YKDEKTCG++  ++ +G   IAEPIG++  I+P TNPTST 
Sbjct: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQY 180
           IFKSLISLKTRN I FSPHPRAK +T  AA  +L AA+ +GAP+++IGWID+PS+EL+  
Sbjct: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180

Query: 181 LMQKADITL--ATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTY 238
           LM   DI L  ATGGP +VK+AYSSGKPAIGVG GNTPV+IDE+A IK AV+S+++SKT+
Sbjct: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240

Query: 239 DNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQS 298
           DNGVICASEQSV+V+ S+Y+ V++ F   G Y+++  EL  V++VI K+G++N  IVGQ 
Sbjct: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300

Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358
           AY IA +AG  VP+ T+ILIGEVT + E EPFAHEKLSP LAMY A +F+DA++KA  L+
Sbjct: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360

Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418
            +GG+GHTS +Y D+     ++  F   MKT R  +N P SQG  GDLYNF++ PS TLG
Sbjct: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420

Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478
           CG WGGNS+SENVGPKHL+N KTVA+R ENMLW ++P  +YF+ G L  AL ++     K
Sbjct: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480

Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTI 538
           RA IVTD   +N  Y D I  +L+   ++ +VF +V  +  L  ++K  E  +SF PD I
Sbjct: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540

Query: 539 IALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAG 598
           IALGG   M +AK+MWV+YEHPE  FE+LA++FMDIRKRIY FPK+G KA ++A+TT++G
Sbjct: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600

Query: 599 SGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIE 658
           +GSEVTPFA+VTD+ TG KY LADY +TP+MAIVDA L+M MPK L A+ G+DA+ +++E
Sbjct: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660

Query: 659 AYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLG 718
           AY SV ASE+++G AL+A++L+ +YLP +Y  G  N  ARE++  A+T+AG+A ANAFLG
Sbjct: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720

Query: 719 LCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIAD 778
           +CHSMA KL S+ +IP G+ANALLI  VI++NA DNP KQ    QY  P    RYA IAD
Sbjct: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780

Query: 779 YIKLG--GNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQ 836
           ++ L   G+    K++ L+  +  LK  L IP SI++AGV E +F +++D++SE A DDQ
Sbjct: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840

Query: 837 CTGANPRFPLTSEIKEMYINCF 858
           CTGANPR+PL SE+K++ ++ +
Sbjct: 841 CTGANPRYPLISELKQILLDTY 862


Lambda     K      H
   0.317    0.134    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: 1829
Number of extensions: 65
Number of successful extensions: 5
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: 862
Length of database: 891
Length adjustment: 42
Effective length of query: 820
Effective length of database: 849
Effective search space:   696180
Effective search space used:   696180
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 (21.6 bits)
S2: 56 (26.2 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

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 paper from 2022 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