GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Klebsiella michiganensis M5al

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate BWI76_RS17250 BWI76_RS17250 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_018413
         (862 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS17250 BWI76_RS17250 bifunctional
           acetaldehyde-CoA/alcohol dehydrogenase
          Length = 891

 Score =  988 bits (2554), Expect = 0.0
 Identities = 487/862 (56%), Positives = 645/862 (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+ +I K+G++N  IVGQ 
Sbjct: 241 DNGVICASEQSVVVVDSVYDAVRERFSSHGGYLLQGQELKAVQNIILKNGALNAAIVGQP 300

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

Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418
            +GG+GHTS +Y D+    +++  F   MKT R  +N P SQG  GDLYNF++ PS TLG
Sbjct: 361 AMGGIGHTSCLYTDQDNQPERVAYFGQLMKTARILINTPASQGGIGDLYNFKLAPSLTLG 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 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLTIVRKGAELANSFKPDVI 540

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

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

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

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

Query: 779 YIKL--GGNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQ 836
           ++ L   G+    K++ L+  + E+K  L IP SI++AGV E +F + +D++SE A DDQ
Sbjct: 781 HLGLTAPGDRTAAKIEKLLGWLDEIKAELGIPKSIREAGVQEADFLAHVDKLSEDAFDDQ 840

Query: 837 CTGANPRFPLTSEIKEMYINCF 858
           CTGANPR+PL +E+K++ ++ F
Sbjct: 841 CTGANPRYPLIAELKQILLDTF 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: 1863
Number of extensions: 70
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: 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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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