GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Paraburkholderia bryophila 376MFSha3.1

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate H281DRAFT_03540 H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16)

Query= metacyc::MONOMER-16246
         (477 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03540 H281DRAFT_03540
           succinate semialdehyde dehydrogenase (EC 1.2.1.16)
          Length = 479

 Score =  311 bits (797), Expect = 3e-89
 Identities = 185/460 (40%), Positives = 253/460 (55%), Gaps = 2/460 (0%)

Query: 10  NYIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAG 69
           +YI G + E A+   V NPA G ++++V    A E  +A+AAA  A   W    A ER+ 
Sbjct: 9   HYIGGEWYEGASTYPVLNPATGEVIAQVAKGGAVEATQAIAAAERAFPAWRSLTAKERSA 68

Query: 70  HLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASD 129
            ++R    +      +A  +T EQGK  + A  EV + A + ++ AE A+R  G++I S 
Sbjct: 69  RVKRWGELMLEHRDALAALLTREQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPSP 128

Query: 130 RPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFAR 189
            P   I + R+P+GVVA I PWNFP  +I RK  PAL  G T+V+KPSEETP +    A 
Sbjct: 129 NPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSALALAV 188

Query: 190 LVAETDLPRGVFNVVCG-AGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNL 248
           L  +  +P GVFNVV G A  +GGAL+    V  +SFTGS   G  +   +A  L KL+L
Sbjct: 189 LAEKAGIPPGVFNVVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLSL 248

Query: 249 ELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMA 308
           ELGG AP IV  DADL+ AV+    S+  N+GQ C C  R YVQ  + + F   +A A  
Sbjct: 249 ELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTLALAQAAR 308

Query: 309 ATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVL 368
             R G+ L + +VE GPLIN+  L K++A V  AL +GA ++TG       G  Y+PTVL
Sbjct: 309 KMRVGNAL-QGDVEQGPLINQAALTKVEAHVADALQKGAKVLTGAKPHALGGTFYEPTVL 367

Query: 369 TGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALREL 428
               +   I +EE FGPV         DEA+A AN   +GL++  +TRDL +A      L
Sbjct: 368 VDASSSMLIAQEETFGPVAACFRFKTEDEAVAAANATPFGLSAYFYTRDLARAWRVGEAL 427

Query: 429 DFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYT 468
           + G   IN            GV++SG+G    K+GL EYT
Sbjct: 428 ESGMVGINEGILSTEVAPFGGVKQSGLGREGSKYGLDEYT 467


Lambda     K      H
   0.320    0.136    0.395 

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: 527
Number of extensions: 23
Number of successful extensions: 3
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: 477
Length of database: 479
Length adjustment: 34
Effective length of query: 443
Effective length of database: 445
Effective search space:   197135
Effective search space used:   197135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

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

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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