GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Desulfovibrio vulgaris Miyazaki F

Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= curated2:Q5L025
         (488 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  234 bits (596), Expect = 1e-65
 Identities = 160/464 (34%), Positives = 240/464 (51%), Gaps = 16/464 (3%)

Query: 10  VLKNYIGGQWVASSGTETLEVPNPAT-GEVLARVPISTKEDVDQAVQAAKKAFATWKDVP 68
           V+  +IGG+ V +   +T+   NPA   EV+ARV    K +VD A++AA+KAF  W+D  
Sbjct: 518 VIPLFIGGKDVTTD--DTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTS 575

Query: 69  VPKRARIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMG 128
              RA  +     +  +   EL+   V E GK + +A+ ++  GI+ +++ A     L  
Sbjct: 576 PADRAMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGT 635

Query: 129 ESLSNIAEEIDSEMFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPIL 188
                 A    + +F  P G+ A I P+NFP  + + M   AIV GN  + KPS     +
Sbjct: 636 PRRMGRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRI 695

Query: 189 ANKLAELFTEAGAPPGVLNVVHGAHEVV-NALIDHEDIRAISFVGSQPVAKYVYERTA-- 245
              L E+F EAG P GV N V G   V+ + L++H  +  I F GS  V   + E+ A  
Sbjct: 696 GYNLTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKV 755

Query: 246 ----AQGKRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGE-N 300
                Q KRV A  G KN  I+  DAD++ AV  V+ SAFG  GQ+C ACS V+++    
Sbjct: 756 QPGQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIY 815

Query: 301 ETFVRRLKQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEM 360
           + FV RL + A  + IG   DP   + PV   S ++ +L Y++   +EG VL+    K  
Sbjct: 816 DRFVERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLV----KRT 871

Query: 361 DDRPEGNFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIY 420
           D   EG ++  TI + + P   IA+EEIF PVL+++RA + DEAL+    +R+     ++
Sbjct: 872 DIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVF 931

Query: 421 TKDAKAVRKFREEADAGMLGINVGVPATMA-FFPFSGWKDSFYG 463
           ++  + + K R E   G L +N G    M    PF G+K S  G
Sbjct: 932 SRSPENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVG 975


Lambda     K      H
   0.319    0.136    0.396 

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: 1047
Number of extensions: 44
Number of successful extensions: 6
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: 488
Length of database: 1013
Length adjustment: 39
Effective length of query: 449
Effective length of database: 974
Effective search space:   437326
Effective search space used:   437326
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: 54 (25.4 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:

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. 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:

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:

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