Alignments for a candidate for aldox-large in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Dinoroseobacter shibae DFL-12

Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate 3607804 Dshi_1212 carbon-monoxide dehydrogenase, large subunit (RefSeq)

Query= SwissProt::Q4J6M3
         (748 letters)



>FitnessBrowser__Dino:3607804
          Length = 806

 Score =  357 bits (915), Expect = e-102
 Identities = 244/776 (31%), Positives = 391/776 (50%), Gaps = 67/776 (8%)

Query: 5   GKSIKRLNDDKFITGRSNYIDDIKIPSLYAG-FVRSPYPHAIIKRIDATDALKVNGIVAV 63
           G S KR+ D +F  G+ NY+DDIK+P +  G FVRSPY HA +  I+A  AL + G+VAV
Sbjct: 20  GSSRKRVEDARFTQGKGNYVDDIKLPGMLHGDFVRSPYAHARVVSINAEAALALPGVVAV 79

Query: 64  FSGKDINPMLKGGVGVLSAYVNPSLFRFKERKAFPEDNKVKYVGEPVAIVIGQDKYAVRD 123
            + KD+ P        LS +  P+L   K+      D KV + G+ VA V+ +D+Y   D
Sbjct: 80  LTAKDLEP--------LSLHWMPTLAGDKQMVL--ADGKVLFQGQEVAFVVAEDRYIAAD 129

Query: 124 AIDRVNVEYEQLKPVIKMEDAEKDEVIVHDELKTNV----------SYKIPFKAGD---I 170
           A++ V VEYE+L  ++   +A + +V++ ++L+             ++   ++ GD    
Sbjct: 130 AVELVEVEYEELPVLVDPFEALQSDVVLREDLEPGADGAHGPRRHHNHIFLWEEGDKAAT 189

Query: 171 EKAFSQADKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEFARI 228
           E+    A+ VV+      R  P P+E  G ++  D     L++W + Q PH  R+  + +
Sbjct: 190 EQVIENAEVVVEEMVYYHRTHPCPLETCGSVASMDKVNGKLTLWGTFQAPHVVRTVASLL 249

Query: 229 FGIPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLASE-AR 287
            GI E  IRV  PD+GG FG+KV +    +  I +SI+  +PV++   R + ++A+  AR
Sbjct: 250 SGIEEHNIRVISPDIGGGFGNKVGVYPGYVCSIVASIVTGKPVKFIEDRMDNLMATAFAR 309

Query: 288 SNVFTGEVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTIIPV----MIPGPYKVRDLE 343
                G ++  K+G + G+   +  D GA+    A   PT  P     +  G Y +    
Sbjct: 310 DYWMKGRISATKEGKITGLHCHVTADHGAF---DACADPTKFPAGFFHICTGSYDIPVAY 366

Query: 344 IESTAVYTTTPPITM-YRGASR-PEATYIIERIMSTVADELGLDDVTIRERNLI--DQLP 399
           +    VYT   P  + YR + R  EA Y IER++  +A EL +D   +R  N I  +Q P
Sbjct: 367 VGVDGVYTNKAPGGVAYRCSFRVTEAAYFIERMIEVLAMELNMDAAELRRINFIRKEQFP 426

Query: 400 YTNPFGLRYDTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHR-------VGVGLAFYLE 452
           YT+  G  YD+GDY   +   +  ++Y  LR   Q ER +  +       +G+GL  + E
Sbjct: 427 YTSALGWEYDSGDYHTAWDKALEAVDYKGLRA-EQAERVEAFKRGETRKLLGIGLTHFTE 485

Query: 453 ICSFGP-----------WEYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPI 501
           I   GP           ++  EI++   G+ +   GT   GQG  T  AQI+A    IP 
Sbjct: 486 IVGAGPVKNCDILGMGMFDSCEIRIHPTGSAVARLGTISQGQGHATTFAQILASETGIPA 545

Query: 502 EKIRVVWGDTDIVEGSFGTYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRY 561
           + I +  GDTD      GTYGSRS  + G+A      ++  K +  AA        ++ +
Sbjct: 546 DSITIEEGDTDTAPYGLGTYGSRSTPVAGAATALAGRKIRAKAQMIAAYLLEVHDNDVEW 605

Query: 562 ENEEFSVKNDPSKKASWDEIASLATTK-----EPIVEKIYYEN--DVTFPYGVHVAVVEV 614
           + + F VK  P +  +  EIA  A  +     EP +E + Y +  ++T+P+G ++ V+E+
Sbjct: 606 DVDRFVVKGAPERFKTIQEIAYAAYNQAIPGVEPGLEAVSYYDPPNMTYPFGAYICVMEI 665

Query: 615 D-DLGMARVVEYRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAIINENGQLSV-TY 672
           D D G   + ++ A DD G  INP + E Q+HGG  + +  A+ ++   ++ G     T 
Sbjct: 666 DVDTGEHEIRQFYALDDCGTRINPMVIEGQVHGGLTEALAIAMGQEIAYDDIGNCKTGTL 725

Query: 673 ADYYVPTAVEAPRFISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDAVGA 728
            D+++PTA E P + + F +   P ++P G KGVGE+  + G  A   A+ DA  A
Sbjct: 726 MDFFIPTAWETPNYTTDFTETPSP-HHPIGAKGVGESPNVGGVPAFSNAVHDAFRA 780


Lambda     K      H
   0.317    0.136    0.390 

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: 1458
Number of extensions: 89
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: 748
Length of database: 806
Length adjustment: 41
Effective length of query: 707
Effective length of database: 765
Effective search space:   540855
Effective search space used:   540855
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: 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)
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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