GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Desulfovibrio vulgaris Miyazaki F

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  212 bits (539), Expect = 6e-59
 Identities = 150/450 (33%), Positives = 222/450 (49%), Gaps = 13/450 (2%)

Query: 20  TDQYEDVVNPATK-EVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRARILFNFQQL 78
           TD      NPA   EV+ +V    K ++D A + A +AF  W   +   RA  L     +
Sbjct: 530 TDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADI 589

Query: 79  LSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLASIATDVEAAN 138
             +   EL+    +E GK   +A  +VG GI+ +++ A    L +G          E  +
Sbjct: 590 ARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHE-MLRLGTPRRMGRAPGELNH 648

Query: 139 YRY-PIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLVELFEKAGL 197
             Y P G+   IAP+NFP  +   M   AI  GN  I KPS     +   L E+F +AGL
Sbjct: 649 LFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGL 708

Query: 198 PKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYKK------GSENLKRVQSL 250
           P+GVFN V G   V+   L EHP++  I F GS  VG  + +K      G    KRV + 
Sbjct: 709 PEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAE 768

Query: 251 TGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVAD 310
            G KN  I+ +DA+L++ V  ++ +AFG  G++C AC+ V V + I D F+ +L +    
Sbjct: 769 MGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQA 828

Query: 311 IKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIFD 370
           IKIG   D   ++GPV     +K  L Y++   +EG  LV   R ++  +G +V  TI +
Sbjct: 829 IKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLV--KRTDIPAEGCYVPLTIVE 886

Query: 371 NVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRENID 430
            +     I ++EIF PVL+V+R  N  EA+ IAN + FA    +F+ +   +   R    
Sbjct: 887 GIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFR 946

Query: 431 AGMLGINLGVPAPMA-FFPFSGWKSSFFGT 459
            G L +N G    M    PF G+K S  G+
Sbjct: 947 VGNLYLNRGSTGAMVERQPFGGFKMSGVGS 976


Lambda     K      H
   0.318    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: 1040
Number of extensions: 52
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: 487
Length of database: 1013
Length adjustment: 39
Effective length of query: 448
Effective length of database: 974
Effective search space:   436352
Effective search space used:   436352
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: 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