Alignments for a candidate for put1 in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Oceanisphaera arctica V1-41

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_104485759.1 UN63_RS05380 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

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



>NCBI__GCF_002936955.1:WP_104485759.1
          Length = 772

 Score = 1026 bits (2652), Expect = 0.0
 Identities = 527/776 (67%), Positives = 619/776 (79%), Gaps = 5/776 (0%)

Query: 6   MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65
           MF A+ V A  Y   +L  L + +T NYIVDE  YL+ L++ VP+S + + ++ +++  L
Sbjct: 1   MFTAATVFASGYAPRDLPSLRQDITRNYIVDENAYLAALLEQVPASGQTLAQINQQSRRL 60

Query: 66  VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125
           V +VR+    G   GIDAFLQQYSL+TQEGIILMCLAEALLRIPD+ TAD LI+DKLSGA
Sbjct: 61  VTRVREESDGG--DGIDAFLQQYSLDTQEGIILMCLAEALLRIPDSHTADELIKDKLSGA 118

Query: 126 KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185
            W  H  +SDS LVNASTWGLMLTGKIV++DKK+DG P+N+L+R++NR+GEP++R AM A
Sbjct: 119 DWARHFRQSDSTLVNASTWGLMLTGKIVRMDKKLDGNPANVLNRMINRMGEPMVRSAMYA 178

Query: 186 AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245
           AMKIMGKQFVLGR +KEALK S   R LGYTHSYDMLGEAA+T  DAEKY +DYANAI  
Sbjct: 179 AMKIMGKQFVLGRDIKEALKASRKSRDLGYTHSYDMLGEAAMTADDAEKYRSDYANAIAT 238

Query: 246 LGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISID 305
           +GA+  N  + PRP+ISIKLSALHPRYE AN +RVLTELY TV+ L++ AR L++ I+ID
Sbjct: 239 VGAEKLNNPKVPRPSISIKLSALHPRYEEANRERVLTELYRTVLGLLEQARKLDVFITID 298

Query: 306 AEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPV 365
           AEE+DRLELSL LF+ L+ +D  +GWG LG+V+QAYSKRALPVL WLT L++ QGDEIPV
Sbjct: 299 AEEMDRLELSLDLFESLYRSDVNQGWGGLGLVIQAYSKRALPVLCWLTALSRSQGDEIPV 358

Query: 366 RLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHN 425
           RLVKGAYWDSE+K  QQ G   YP+YTRKA TDVSYLACARYLLSDAT GAIYPQFA+HN
Sbjct: 359 RLVKGAYWDSEIKHCQQTGIDGYPVYTRKASTDVSYLACARYLLSDATDGAIYPQFATHN 418

Query: 426 AQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRR 485
           A TV ++  MAG+RN EFQRLHGMG+ELY+ +L+E      RIYAP+GAHKDLLPYLVRR
Sbjct: 419 AHTVVSVMAMAGERNFEFQRLHGMGEELYNAVLAENPGLNCRIYAPVGAHKDLLPYLVRR 478

Query: 486 LLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGL 545
           LLENGANTSFVHKLVDPKTPI++L+ HPL +L  Y++LAN+KI LP  IF  DR NS+GL
Sbjct: 479 LLENGANTSFVHKLVDPKTPIDTLITHPLTSLAEYRSLANDKIPLPLAIF-PDRANSRGL 537

Query: 546 NMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTL-TGEHKTVVSPFDTTQTVGQVAFADK 604
           NMNI     PFF ALD+     WQAGP+V G+TL TG    V+SP D  Q VGQV FADK
Sbjct: 538 NMNIEGIRAPFFKALDELTIKTWQAGPVVGGKTLTTGAANAVLSPQDHGQQVGQVYFADK 597

Query: 605 AAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGID 664
           A +E AV  A AAF  W  TPVEVRA AL+KLADLLEEN   LI+LCTREAGK +QDGID
Sbjct: 598 ATVELAVGKAQAAFKGWRNTPVEVRAQALEKLADLLEENHIPLISLCTREAGKLLQDGID 657

Query: 665 EVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQ 724
           EVREAVDFCRYYA +A+ LM +P+ LPG TGELN L+ QGRG FVCISPWNFPLAIFLGQ
Sbjct: 658 EVREAVDFCRYYANEARTLM-EPKKLPGYTGELNLLYAQGRGPFVCISPWNFPLAIFLGQ 716

Query: 725 VSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA 780
           V+AALA GNTV+AKPAEQTS+I + AV LAH+AGIP DVLQ LPG GATVG  LTA
Sbjct: 717 VAAALATGNTVLAKPAEQTSLIAHLAVTLAHKAGIPADVLQLLPGDGATVGATLTA 772


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: 1914
Number of extensions: 81
Number of successful extensions: 5
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: 772
Length adjustment: 43
Effective length of query: 1021
Effective length of database: 729
Effective search space:   744309
Effective search space used:   744309
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: 56 (26.2 bits)

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_146084721.1 UN63_RS06480 aldehyde dehydrogenase family protein

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



>NCBI__GCF_002936955.1:WP_146084721.1
          Length = 286

 Score =  393 bits (1010), Expect = e-114
 Identities = 197/285 (69%), Positives = 236/285 (82%), Gaps = 1/285 (0%)

Query: 778  LTADERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVND 837
            LTAD RI GVCFTGST TA LIN+TLA R+GAIIPLIAETGGQNAM+VDST+ PEQVV D
Sbjct: 1    LTADPRIAGVCFTGSTDTAMLINQTLAKRKGAIIPLIAETGGQNAMIVDSTALPEQVVRD 60

Query: 838  VVSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATA 897
            VV ++F SAGQRCSALRVL+LQ+DIA+RV+++L+GAMDEL + +P+   TDVGPVID  A
Sbjct: 61   VVRAAFQSAGQRCSALRVLYLQDDIAERVLEILKGAMDELSVADPALWSTDVGPVIDQDA 120

Query: 898  KANLDAHIDHIKQVGK-LIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIR 956
            +A L+AH+  +   GK +I Q  L  G + G ++ PTA+EI +I  LEKE FGPILHV+R
Sbjct: 121  QAGLEAHLSKMLAAGKKVIAQTRLGKGCDKGFYIQPTALEISAIGELEKEQFGPILHVVR 180

Query: 957  YKASELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPF 1016
            +KA ++  VI++IN+TG+GLTLGIHSRNE  A  VA  +N GN YINR+QIGA+VGVQPF
Sbjct: 181  FKAKDIDLVINDINNTGYGLTLGIHSRNESFAEYVAQSINAGNAYINRDQIGAMVGVQPF 240

Query: 1017 GGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGD 1061
            GGQGLSGTGPKAGGPHYLTRF+TEKT TNN TAIGGNATLLSLG+
Sbjct: 241  GGQGLSGTGPKAGGPHYLTRFITEKTITNNTTAIGGNATLLSLGE 285


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: 787
Number of extensions: 33
Number of successful extensions: 2
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: 286
Length adjustment: 35
Effective length of query: 1029
Effective length of database: 251
Effective search space:   258279
Effective search space used:   258279
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 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