Alignments for a candidate for put1 in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Maridesulfovibrio zosterae DSM 11974

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_027721414.1 H589_RS0107295 proline dehydrogenase family protein

Query= reanno::ANA3:7023590
         (1064 letters)



>NCBI__GCF_000425265.1:WP_027721414.1
          Length = 1012

 Score =  393 bits (1010), Expect = e-113
 Identities = 284/961 (29%), Positives = 482/961 (50%), Gaps = 82/961 (8%)

Query: 128  DEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAM 187
            +E+ +  DS + +   WG   TG               L+++++N+         + + +
Sbjct: 75   EEYFAGDDSNIPDVLKWGASKTG-----------FGGGLVAKVLNK--------TIRSNI 115

Query: 188  KIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITEL- 246
            + M +QF++G+  KEA+K     RK G+    D+LGEA ++ ++A  Y   Y   +  + 
Sbjct: 116  EGMARQFIIGQKAKEAVKGIRKLRKDGFAFVLDLLGEATVSHEEAIAYREGYLEVLDAIE 175

Query: 247  -------GAQSYNE---NESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLAR 296
                   G  S  +     +P+  +++K SA + + +  + +  +  + D++  + +   
Sbjct: 176  KEYKKWDGLDSSTDLDWGHAPKINVAVKPSAFYSQAKPVDLEGTVQGMMDSIEPVYQKVM 235

Query: 297  GLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLA 356
             +   + ID E +   E ++++F++L        +  LGIV QAY K     +  +   A
Sbjct: 236  NMGGFMCIDMEALKYKEPTVEMFKRL--RKKYSDYPHLGIVFQAYLKTVDEDVSSMIEWA 293

Query: 357  KEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGA 416
            +E+   I +RLVKGAYWDSE   A+Q  +   P++T K  +D++Y   AR++L +     
Sbjct: 294  REENLPISIRLVKGAYWDSETVIAKQ-NDWPVPVWTHKPESDMAYERVARFILEN--HDI 350

Query: 417  IYPQFASHNAQTVAAISDMAGDRN-----HEFQRLHGMGQELYDTILSEAGAKAVRIYAP 471
             +   ASHN +T+A++ + A + +     +EFQ L+GM + +   + + A  K VR+Y P
Sbjct: 351  CHFACASHNIRTIASVMETANELSVPEDKYEFQVLYGMAEPVRKGLRNVA--KRVRLYCP 408

Query: 472  IGAHKDLLP---YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKI 528
             G   DL+P   YLVRRLLEN AN SF+ +    +  +  L+ +P+KTL   + LAN   
Sbjct: 409  YG---DLIPGMAYLVRRLLENTANESFLKQTFADEADVNILLENPVKTLE--RELANKPA 463

Query: 529  VLPTDIFGSDRKNSKGLNMNII-------------SEAEPFFAALDKFKSTQWQAGPLVN 575
              P       R   KG++  ++              E + F +++ K +    Q  PL  
Sbjct: 464  PRP-----DTRPRMKGVDGELVPFNNFPPSDFTLKDERDGFPSSMSKIRQNIGQRYPLYI 518

Query: 576  G--QTLTGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTPVEVRASAL 633
            G  + +T +     +P D ++ +G V  A  A +++AVA+A  A+  W       RA  L
Sbjct: 519  GGQEIVTDDTLDSYNPADPSEILGTVCQAGVAEVDKAVATAKEAYLDWRNITPRERAQYL 578

Query: 634  QKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMSKPELLPGP 693
             K A   ++N  EL AL   E GK       ++ E +DF  YYA +  +L   P+ +   
Sbjct: 579  LKAAKYCKDNIHELSALQVLEVGKQWDQAQGDIAEGIDFLEYYAREMIRL-GDPKRMGNA 637

Query: 694  TGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQL 753
             GE  + F QG+GV   I+PWNFP AI +G VSAA+ AG  VV KPA  +S++GY  V++
Sbjct: 638  PGEYAQYFYQGKGVAAVIAPWNFPFAISVGMVSAAIVAGCPVVYKPAGISSVVGYGLVEM 697

Query: 754  AHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLAN---REGAI 810
               AG+P  V  Y+PG G+ +G+ L     I  + FTGS      I    A     +   
Sbjct: 698  FKAAGLPDGVFNYIPGRGSVMGDHLVDHPDISVIAFTGSMEVGLRIQERAAKVHPGQEHC 757

Query: 811  IPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADRVIDVL 870
              +IAE GG+N +++D  +  ++ V  V+ ++F   GQ+CSA   + + + I DR    L
Sbjct: 758  KRVIAEMGGKNGIIIDDDADLDEAVLGVLYAAFGFQGQKCSACSRVIVVDSIYDRFTHRL 817

Query: 871  QGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMSLPAG-TENGHF 929
            + A + + +G        +GPV+D  A+ N+  + +  ++ GK++ +   PA   + G  
Sbjct: 818  KEAANSVKLGPAEDPSNYMGPVVDKAAQKNVLEYCEIAEKEGKVLVKHEAPAEYLDKGGC 877

Query: 930  VSPTAVEIDSI----KVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNE 985
             +P  + ++ I    ++ ++E FGP+L V+R  A +    I+  NST F LT  ++SR+ 
Sbjct: 878  YTPMLI-VEGITKEHRIAQEEVFGPVLSVMR--AKDFEEAIEIANSTKFALTGAVYSRSP 934

Query: 986  GHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTN 1045
             H      +  VGN+Y+N+  +GA+V    FGG  +SG G K+GGP YL +F+  +    
Sbjct: 935  KHLDLATREFRVGNLYLNKPSVGALVERHSFGGFKMSGVGSKSGGPDYLLQFMDPRLVCE 994

Query: 1046 N 1046
            N
Sbjct: 995  N 995


Lambda     K      H
   0.317    0.133    0.377 

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: 2109
Number of extensions: 109
Number of successful extensions: 8
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: 1064
Length of database: 1012
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 967
Effective search space:   985373
Effective search space used:   985373
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: 57 (26.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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 2024 update 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