Aligments for a candidate for aldox-large in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for aldox-large in Phaeobacter inhibens BS107

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate GFF2054 PGA1_c20870 molybdenum hydroxylase family protein, large subunit

Query= metacyc::MONOMER-18071
         (749 letters)



>lcl|FitnessBrowser__Phaeo:GFF2054 PGA1_c20870 molybdenum
           hydroxylase family protein, large subunit
          Length = 787

 Score =  445 bits (1144), Expect = e-129
 Identities = 270/764 (35%), Positives = 418/764 (54%), Gaps = 44/764 (5%)

Query: 2   SYVGKPVKRIYDDKFVTGRSTYVDDIRIPA-LYAGFVRSTYPHAIIKRIDVSDALKVNGI 60
           S +G   KR  D +F+TG   Y DDI +    Y  F+RS   H  +  +D SDA  + G+
Sbjct: 5   SGIGASPKRREDVRFLTGTGNYTDDINMRGQAYVHFLRSDVAHGRLTSVDTSDAAAMPGV 64

Query: 61  VAVFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFP---ENKVKYVGEPVAIVLGQDK 117
           V +FT  +   +  GG+ P    +  R     +  A P   + KV++VG+P+A V+ +  
Sbjct: 65  VRIFTGADFEGV--GGL-PCGWQVTDRHGEVMQEPAHPVLAQGKVRHVGDPIAAVVAETP 121

Query: 118 YSVRDAIDKVVVEYEPLKPVIRMEEAEKDQVI-IHEELKTNISYKIPF---KAGEVDKAF 173
              RDA + +V++ E L  VI M+EA KD    +H++L +N+ Y   F     G VDKA 
Sbjct: 122 EQARDAAEAIVLDIEDLPAVINMKEAVKDGATKVHDDLTSNLCYDWGFVEENRGAVDKAI 181

Query: 174 SESDKVVRVEAINERLIPNPMEPRGIVSRFE--AGTLSIWYSTQVPHYMRSEF-ARILGI 230
            ++  V  +E +N RL+ NPMEPR  V  F    G  +++ ++Q PH +R    A +LGI
Sbjct: 182 KDAAHVTTLELVNNRLVANPMEPRVAVGDFNRATGDSTLYTTSQNPHVIRLLMGAFVLGI 241

Query: 231 PESKIKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNV 289
           PE K++V  PDVGG FG+K+    EE     ++  L R V+WT++RSE  ++ +  R +V
Sbjct: 242 PEHKLRVVAPDVGGGFGSKIFHYAEEAFCTFAAKALNRAVKWTSSRSEAFMSDAHGRDHV 301

Query: 290 FTGEVAVKRDGTILGIKGKLLLDLGAYITVTAGIQPLIIP-MMIPGPYKIRNLDIESVAV 348
              E+A+  D     ++ +   ++GAY++  A   P  +   ++ G YK   + +   AV
Sbjct: 302 TKIELALDADNNFTALRTETYANMGAYLSTFAPSVPTWLHGTLMAGNYKTPLIYVNVKAV 361

Query: 349 YTNTPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTELPYTNPFGLRYD 408
           +TNT  +  YRGA RPEATY +ER++   A ELG+D +++R +N +TE PY  P  + YD
Sbjct: 362 FTNTVAVDAYRGAGRPEATYQLERVIDKAARELGVDPIALRRQNFITEFPYATPVAVEYD 421

Query: 409 SGDYVGLLR--EGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP--------- 457
           +GDYV  +   E +  L  ++ ++ A   + KG   G+G+  Y+E C   P         
Sbjct: 422 TGDYVATMDKLEEIADLSGFDARRAAS--KAKGKLRGLGVNCYIEACGIAPSNLVGQLGA 479

Query: 458 ----WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTV 513
               +E A VRV+  G ++V+TG+  HGQG ET+  Q++AD + I    V +  GDTD  
Sbjct: 480 RAGLYESATVRVNATGGIVVMTGSHSHGQGHETSFPQVIADMIGIPEDMVEIEHGDTDKA 539

Query: 514 AASMGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSK 573
              MGTYGSRS+ +GGSA ++  EKI+ K K+IAA        +++ + G+F +     K
Sbjct: 540 PMGMGTYGSRSLAVGGSAMVRATEKIIAKAKKIAAHILEASDADIELKDGQFTVAG-TDK 598

Query: 574 KMSWDDVASIAYRSH-------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVL 624
            ++W DV   AY  H       +PGL E   Y+  + T+P G +   VEVD DTG   + 
Sbjct: 599 SLAWGDVTLAAYVPHNYPLEDIEPGLEETAFYDPANFTYPSGAYACEVEVDPDTGKVTIE 658

Query: 625 EYRAYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQLI-VTYADYYVPTAVE 683
            + A DD G +VNP + + Q+HGG  Q +GQAL E  + +++GQL+  ++ DY +P A +
Sbjct: 659 RFAAADDFGNIVNPMIVDGQVHGGIGQGIGQALLEGCVYDDDGQLLSASFMDYAMPRADD 718

Query: 684 APKFTSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAI 727
            P +    + Q   ++ P G KG GEA  I  P  ++ A+ DA+
Sbjct: 719 LPFYKVDHSCQTPCTHNPLGVKGCGEAGAIGTPPAVVNAVVDAL 762


Lambda     K      H
   0.317    0.136    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: 1407
Number of extensions: 73
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: 749
Length of database: 787
Length adjustment: 41
Effective length of query: 708
Effective length of database: 746
Effective search space:   528168
Effective search space used:   528168
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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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, 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

GapMind for catabolism of small carbon sources