Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas fluorescens GW456-L13

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate PfGW456L13_2092 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

Query= metacyc::MONOMER-20833
         (739 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2092
          Length = 773

 Score =  340 bits (872), Expect = 2e-97
 Identities = 254/777 (32%), Positives = 383/777 (49%), Gaps = 83/777 (10%)

Query: 13  NLSRRRFLAST-AVGALVIGFGLPLGAGRVQAATSAERGTQVPA-------------FLE 58
           NLSRR FL    A GALV+       +   Q A + E+  +  A             ++ 
Sbjct: 12  NLSRRGFLKGVGATGALVVA-----ASWGWQDAFAEEKEKKFGADGMPHGWFDDPKVYVS 66

Query: 59  IRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRIT 118
           I  DGTV ++    E GQG  T++  +V +EL+AD A   V+ AP  E    +  G + T
Sbjct: 67  IAADGTVTVICNRSEMGQGVRTSLTMVVADELEADWAMVKVQQAPGDE----VRFGNQDT 122

Query: 119 GGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGEL 178
            GS S+R  Y  MRR GA ARAML QA A QW V VGE   Q  +V+H  SGR LGYG L
Sbjct: 123 DGSRSMRHWYEPMRRCGAAARAMLEQAAADQWKVSVGECQAQLHKVIHKPSGRELGYGAL 182

Query: 179 ASSALDMPVPDPASITLRDPSQFRWIGKP-VKRLDAYDKSTGKALYSIDLKVDNMLHAAV 237
           A++A  + VP   S+ L+ PS+FR+IGK   K +D  D   G+A+Y  D+  D ML+A +
Sbjct: 183 AAAAGALAVPARESLRLKQPSEFRYIGKEGTKAIDGEDIVNGRAVYGADVHFDGMLYATI 242

Query: 238 QHAPRLGMTVGSLRNQS--QVEGMKGVHSVHVLP--------GAVAVVAERWWHAKRAVE 287
                 G  V S    +  +V G+  V  +   P        G +AVVA   W A +  E
Sbjct: 243 ARPTVYGGKVKSFDGSAAMKVPGVVKVVQIESRPLPSEFQPLGGIAVVASNTWAAIKGRE 302

Query: 288 AIQVDWQEAAADSALRVMPADFSSDKHR-EFLAAQQGPTRDDENEGDVAGALKGAKTQVE 346
           A++++W +           A + S  +R E  AA   P +     G++  A+  A + +E
Sbjct: 303 ALKIEWDDGP--------NASYDSIAYRKELEAASLKPGKVVRKTGNLDEAMASADSTLE 354

Query: 347 ATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSP 406
           A+Y+  +L+ + +EP  A+ARF  DG  + W P+QAP + R  I +R GL   ++T +  
Sbjct: 355 ASYYLPHLSQSPMEPMVAIARFK-DGACQAWGPSQAPQVTRERIGERLGLPFDKVTFNVT 413

Query: 407 LLGGFFGRHFLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALD 466
           LLGG FGR    D       AI   +   + +++ W+RE++        ++    +A+L+
Sbjct: 414 LLGGGFGRKSKPDFI--IEAAILAKEFPGKAVRVQWTREDDIHCSYFHTVSAEYLKASLN 471

Query: 467 DKGLPVAIEAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPML 526
             GLP      +     T   A     +       G +  +YAIPN R+          +
Sbjct: 472 KDGLPSGWLHRTVAPSITALFAPGMNHEAAFELGMGFTNMAYAIPNIRLENPEATVHTRV 531

Query: 527 GYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLR--------------------- 565
           G++RSV N  + F  +SF+DELA K G DP + ++ LL                      
Sbjct: 532 GWYRSVSNIPHGFAIQSFIDELAHKAGQDPLKYQIRLLGPDRQIDPRTLSEEWNYGESPE 591

Query: 566 ----DNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSI-E 620
               D  RL T+L+ A + + GW R     E    R  G+A+   F ++ AA+ EV + +
Sbjct: 592 RYPIDTARLRTVLETAAK-AAGWGR-----ELPKGRGLGLAVHYSFVTYVAAVIEVEVKD 645

Query: 621 NGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYP 680
           +G + VH    A+D G  +NP  + AQ  GA  +GL   +L E  + DGK +  N+ +Y 
Sbjct: 646 DGTLVVHKADIAVDCGPQINPERIRAQFEGACVMGLGNAVLGEISFKDGKVQQDNFHMYE 705

Query: 681 I----LAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           +    LAP ++A VH+        +GG+GEP +P +APA+ NA+   TG+R+R+LP+
Sbjct: 706 VARMSLAPKEVA-VHLVTPPGDVPLGGVGEPGVPPIAPALCNAIFAATGKRIRNLPV 761


Lambda     K      H
   0.317    0.134    0.394 

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: 1355
Number of extensions: 71
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 739
Length of database: 773
Length adjustment: 40
Effective length of query: 699
Effective length of database: 733
Effective search space:   512367
Effective search space used:   512367
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: 55 (25.8 bits)

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

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Candidates (tab-delimited)
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
the source code
instructions for running GapMind on your computer

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