GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Lactobacillus silagei IWT126

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_089136810.1 CES79_RS07645 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_018413
         (862 letters)



>NCBI__GCF_002217945.1:WP_089136810.1
          Length = 873

 Score =  705 bits (1819), Expect = 0.0
 Identities = 387/860 (45%), Positives = 567/860 (65%), Gaps = 19/860 (2%)

Query: 3   VTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLV 62
           V+  + +D  +    +A      ++QE VD I    A+A +D  + LAK AV ETG G+ 
Sbjct: 18  VSVNEHIDALVNKAHDALCGMDDFTQEKVDHIVHQMAIAGLDQHMRLAKLAVDETGRGVW 77

Query: 63  EDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIF 122
           EDK IKN FA E I++  K++KT GIIE ++   + K+AEP+G++A + PVTNPTSTT+F
Sbjct: 78  EDKAIKNMFATEEIWHSIKNDKTVGIIEDDKERQLIKVAEPLGILAGVTPVTNPTSTTMF 137

Query: 123 KSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLM 182
           KSLI++KTRN I F  HP+A+KS++ AAK + DAA+ +GAPE +I WI+EPS+E T  LM
Sbjct: 138 KSLIAVKTRNPIIFGFHPQAQKSSVAAAKVMRDAAIAAGAPEGVIQWIEEPSLEATTALM 197

Query: 183 Q--KADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDN 240
              K    LATGGP +VK+AYS+GKPA+GVGPGN P  I+++A+IK AV+ I+LSKT+DN
Sbjct: 198 NHPKVASVLATGGPGMVKAAYSTGKPALGVGPGNGPAYIEKTANIKRAVNDIVLSKTFDN 257

Query: 241 GVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIF--KDGSVNPKIVGQS 298
           G+ICA+E SVI+   IYN VK E + R  + IKK +   + + ++  K GSV   I G +
Sbjct: 258 GMICATENSVIIDADIYNDVKQEMKARKVFFIKKADQKALADAMYDPKRGSVKGPIAGMA 317

Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358
           A  IA +AGI VP+ T++L  E+T++G +   + EKL PV+++Y++ +  +  K A  L+
Sbjct: 318 AVKIAKLAGIDVPEDTKVLAAELTTVGPDNMLSAEKLCPVISVYKSADHKEGFKIANDLL 377

Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418
           + GGLGHT+ I+ ++    D    +   MK  R  VN P++ G  G+LYN  I PS TLG
Sbjct: 378 HFGGLGHTAAIHTED---EDLATEYGIKMKASRVLVNTPSALGGIGNLYNEMI-PSLTLG 433

Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478
            G WG NSVS NV    LLNIKT+A+RR NM W ++P +VYF+   +++ L  +  +KK 
Sbjct: 434 TGSWGKNSVSHNVSSFDLLNIKTIAKRRNNMQWIKLP-RVYFEKTSVRY-LGSMPGVKK- 490

Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHL--DIDFKVFNKVGREADLKTIKKATEEMSSFMPD 536
            AFIV D    +L YVD ++  L+     I++++F+ +  +    T++K   +M +F PD
Sbjct: 491 -AFIVADPAMISLGYVDKVLGELKRRPDGIEYQLFSVMESDPTTDTVEKGYAQMKAFKPD 549

Query: 537 TIIALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTS 596
           TIIALGG   M +AK MW+ YEHP+  F     KF+DIRKR Y F K  KKA  VAI T+
Sbjct: 550 TIIALGGGSPMDAAKCMWLFYEHPDASFFGAKQKFLDIRKRTYQFEK-AKKAQFVAIPTT 608

Query: 597 AGSGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNS 656
           +G+GSEVTPFA++TD+ T  KY LADY +TP++AIVD++ +  +PK   +++G+D L + 
Sbjct: 609 SGTGSEVTPFAVITDSKTHVKYPLADYALTPDVAIVDSQFIESLPKKTISWAGLDVLTHG 668

Query: 657 IEAYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAF 716
           IE++ S  AS+YT   +L+AI+L+F  L  +Y NG  ++ ARE+M +A+T+AGMA ANAF
Sbjct: 669 IESFVSNMASDYTRPWSLQAIKLVFDNLTASY-NG--DQHAREEMHNAATIAGMAFANAF 725

Query: 717 LGLCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARI 776
           LG+ HS+A KL  E  +P G+A A+ +  VI++N    P K    P+Y+Y      YA I
Sbjct: 726 LGVNHSIAHKLGGEFGLPHGLAIAITLPHVIRYN-FKEPRKLTTWPKYEYFRADEDYAEI 784

Query: 777 ADYIKLGGNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQ 836
           A Y+ L G  +EE  + L++KI +L  ++++  S+K  GV +++F   +D ++ELA +DQ
Sbjct: 785 ARYVGLTGKNNEELKEALVHKIIDLAHSVDVTLSLKANGVDKKHFDEKVDDLAELAYEDQ 844

Query: 837 CTGANPRFPLTSEIKEMYIN 856
           CT ANP+ PL  E++++ I+
Sbjct: 845 CTTANPKEPLIGELRQIMID 864


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: 1773
Number of extensions: 84
Number of successful extensions: 11
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: 873
Length adjustment: 42
Effective length of query: 820
Effective length of database: 831
Effective search space:   681420
Effective search space used:   681420
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 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