Alignments for a candidate for drdehyd-beta in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Azospirillum brasilense Sp245

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate AZOBR_RS30030 AZOBR_RS30030 twin-arginine translocation pathway signal protein

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



>FitnessBrowser__azobra:AZOBR_RS30030
          Length = 729

 Score =  382 bits (982), Expect = e-110
 Identities = 271/736 (36%), Positives = 383/736 (52%), Gaps = 37/736 (5%)

Query: 15  SRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGTQVP---AFLEIRPDGTVRLLSPF 71
           SRR FL   A GALV+G  LP      +AA     G   P   AF+ I  D TV +L   
Sbjct: 12  SRRGFLKG-AGGALVLGAMLPRTGFASEAAAPKVVGPADPRPQAFIRIAADDTVTVLVKH 70

Query: 72  MEGGQGTHTAMAQIVGEELDADPATFIVEAAPP-GEAYVVMENGLRITGGSMSVRMSYPT 130
           ++ GQG  T +  IV EELDAD A      AP  G  Y     G++ TGGS +V  S+  
Sbjct: 71  LDKGQGIMTGLTTIVAEELDADWAQMRGAFAPADGALYANHFFGIQGTGGSTAVANSWDE 130

Query: 131 MRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDP 190
           +R  GA ARAML+   A +W VP   +T + G V HAAS RS  +GELA  A  +PVP  
Sbjct: 131 LRMAGAAARAMLVATAAARWSVPASPVTVEQGVVRHAASNRSARFGELAEDAAKLPVPQ- 189

Query: 191 ASITLRDPSQFRWIGKP-VKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGS 249
            ++ L+D   ++ IG P + RLD   K+ G A++++D++    + A +  +PR G TV S
Sbjct: 190 -NVALKDAKDYKLIGNPSLHRLDHVSKTDGTAIFAMDIRRPGQVTAVLARSPRFGGTVKS 248

Query: 250 LRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADS-ALRVMPAD 308
           + + +  + + GV  V  LP  VAVVA   W A +  EA+ V+W +A A+      M AD
Sbjct: 249 V-DAAAAKQVPGVLEVLTLPMGVAVVARNTWAAMKGREALTVEWDDAKAEMRGTEEMLAD 307

Query: 309 FSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARF 368
           +        LA Q G    D   GD A AL GA   VEA +   YL HA +EP +A    
Sbjct: 308 YRK------LADQPGNVATDT--GDAAKALAGAAKVVEAEFVFPYLAHAPMEPLNATVEL 359

Query: 369 NPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAI 428
            PDG   IW  +Q   + +   A   G  P Q+ +++   GG FGR    D A+   +A+
Sbjct: 360 TPDGGCTIWAGSQFQGVEQKVAAGILGCKPEQVVINTVWAGGSFGRRATPD-ADYIAEAV 418

Query: 429 ALAKAVS--RPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVA----IEAVSATEG 482
            +AKA     P+ L+W+RE++      RPL + K +A LD  G  VA    I   S   G
Sbjct: 419 TIAKAYGGKAPVHLVWTREDDIRGGRYRPLFLHKVKAGLDASGTLVAWRQSIVGQSFMIG 478

Query: 483 PT-EALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLG-YWRSVGNSLNDFF 540
              E    K G  +D T+VEG S  +Y +PN  +  ++   +P+   +WRSVG++   + 
Sbjct: 479 TLFEGFMVKNG--VDATSVEGSSDMAYTVPNLHV-DLHSPPSPVTTLWWRSVGHTHTAYA 535

Query: 541 YESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARG 600
            E  +DELA   G DP   RL +L+D+PRL  +L+ A E +G  +  P        + RG
Sbjct: 536 KEVMIDELAAAAGKDPVAFRLEMLKDHPRLQGVLKLAAEKAGWGQPLP------KGKGRG 589

Query: 601 VAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQT 659
           +A+   F S  A +AEVS+ E G+V +  +  A+D G +VNP IVEAQV+G     +   
Sbjct: 590 IAVHESFSSFVAHVAEVSVDEQGRVTIDRVVCAVDCGQVVNPNIVEAQVSGGTGWAIGHA 649

Query: 660 LLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANA 719
           L +E     G     N+D Y  L  ++M  + V ++ S  +  G+GEP +P  APAVANA
Sbjct: 650 LRDEITLTGGLVDQSNFDAYQPLRNSEMPPIEVHILPSTARPTGVGEPGVPTAAPAVANA 709

Query: 720 VAQLTGQRVRSLPLSR 735
           V   TG+R+  LP +R
Sbjct: 710 VFAATGKRLHHLPFTR 725


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: 1316
Number of extensions: 68
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: 739
Length of database: 729
Length adjustment: 40
Effective length of query: 699
Effective length of database: 689
Effective search space:   481611
Effective search space used:   481611
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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