GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lacA' in Echinicola vietnamensis KMM 6221, DSM 17526

Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Echvi_1439 Echvi_1439 Choline dehydrogenase and related flavoproteins

Query= reanno::Pedo557:CA265_RS15345
         (567 letters)



>lcl|FitnessBrowser__Cola:Echvi_1439 Echvi_1439 Choline
           dehydrogenase and related flavoproteins
          Length = 566

 Score =  733 bits (1893), Expect = 0.0
 Identities = 351/569 (61%), Positives = 425/569 (74%), Gaps = 6/569 (1%)

Query: 2   MNLNTNLKAENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKNP 61
           MNLN     ENTYDAIV+GSGISGGWAAKEL EKGL+ L+LERG N+EHI GY T   NP
Sbjct: 1   MNLNIKATKENTYDAIVVGSGISGGWAAKELCEKGLKTLVLERGKNVEHIKGYPTTNLNP 60

Query: 62  WDFKHAGKLTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKS 121
           W+  H G  T E K  HP+Q R Y + E  +++WVNDLE PY E K F+W RG+HVGG+S
Sbjct: 61  WELDHRGWSTNESKEKHPIQSRCYAFGEDTQQFWVNDLENPYNEVKPFNWLRGYHVGGRS 120

Query: 122 LMWGRQSYRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDG 181
           LMWGRQ YRLSD +FE NA+DG+G DWPVRY +L+PWY Y E+FAGISG  E  P  PD 
Sbjct: 121 LMWGRQCYRLSDIDFEANAKDGYGVDWPVRYKDLAPWYTYVEKFAGISGQAEGLPQLPDS 180

Query: 182 QFLPPMDLNIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKGRGNCQYRNLCSRGCPFG 241
            FLP M++N VEK V AR++E +  +RI+ IGR A+ T    GRG CQYRNLC+RGCPFG
Sbjct: 181 HFLPAMEMNCVEKHVAARVKEKFD-DRIITIGRAAHATAALNGRGPCQYRNLCARGCPFG 239

Query: 242 AYFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIV 301
            YFS+ S+TLPAAM T  +TLRP+SIV  ++YDK+T KA GV ++DAET +  E+YAK+V
Sbjct: 240 GYFSSNSATLPAAMQTGNMTLRPFSIVTEVLYDKETGKANGVRIMDAETKEYTEYYAKVV 299

Query: 302 FVNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGR 361
           F+N STLG+ ++LLNS S+A PNGLGNGS Q+GHNLMDHH+  GASG  EGF DKY YGR
Sbjct: 300 FLNASTLGTAWILLNSVSDAFPNGLGNGSEQVGHNLMDHHYGVGASGAIEGFGDKYYYGR 359

Query: 362 RANGIYIPRYQNI--GNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGK- 418
           R NGIY+PR++NI    ++ DY+RGFGYQGGA R   QG  A    GAD K   T P + 
Sbjct: 360 RPNGIYVPRFRNISEATERPDYVRGFGYQGGAGRGRGQGGPA--GVGADFKLSKTQPSED 417

Query: 419 WSMGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEMLE 478
           WS G+G +GE LPYY+NKV ++  K D +G P L IDCE+KENE  MR DM   A ++LE
Sbjct: 418 WSFGIGSWGEHLPYYDNKVSLNHDKLDAYGLPTLDIDCEFKENEMAMRKDMRQSAVDILE 477

Query: 479 KAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMPSI 538
             G KNI ++D+   PG  IHEMGTARMG DPKTSVLN +NQMHEV NV++TDG+ M S 
Sbjct: 478 AVGAKNINSYDSAPPPGHCIHEMGTARMGKDPKTSVLNGYNQMHEVPNVYITDGAFMASS 537

Query: 539 ACQNPSLTFMALTARACDYAVKELKKKNI 567
           ACQNPSLT+MA TARACD+AVKELKK+N+
Sbjct: 538 ACQNPSLTYMAFTARACDHAVKELKKQNL 566


Lambda     K      H
   0.317    0.134    0.421 

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: 1117
Number of extensions: 51
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: 567
Length of database: 566
Length adjustment: 36
Effective length of query: 531
Effective length of database: 530
Effective search space:   281430
Effective search space used:   281430
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: 53 (25.0 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 (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 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