Alignments for a candidate for put1 in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Pseudomonas litoralis 2SM5

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_090274943.1 BLU11_RS15565 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

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



>NCBI__GCF_900105005.1:WP_090274943.1
          Length = 1072

 Score = 1196 bits (3094), Expect = 0.0
 Identities = 615/1058 (58%), Positives = 780/1058 (73%), Gaps = 9/1058 (0%)

Query: 9    ASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNK 68
            A E+L    +  NL +L +  +  Y+VDE+  + ELI+L+      I+++ +    LV +
Sbjct: 18   ADELLHPDLEQQNLQQLAQKASQYYMVDEDTLMPELIQLLDHQPAHIKQLHQSTAVLVQR 77

Query: 69   VRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGAKWD 128
            VR   +   +  +D  LQQYSL+TQEG++LMCLAEALLRIPD+ TA+ALI DKLS A W 
Sbjct: 78   VRS--QGDAVDSLDQLLQQYSLDTQEGVLLMCLAEALLRIPDSRTAEALIRDKLSVADWK 135

Query: 129  EHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMK 188
             HL +SDS+LVNASTWGL+LT  +VK+D + D  P  +L+RLV+RLGEPV+RQ M  AMK
Sbjct: 136  SHLGQSDSLLVNASTWGLILTKGLVKMDPR-DDQPVPVLNRLVSRLGEPVVRQVMSHAMK 194

Query: 189  IMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITELG- 247
            +MG QFVLGR + EAL N +   K GYT+S+DMLGEAA TR+DA++YF  Y +AI  +G 
Sbjct: 195  LMGHQFVLGRNLPEALNNGKSLFKQGYTYSFDMLGEAARTREDAQRYFAAYLDAIERVGQ 254

Query: 248  AQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISIDAE 307
            A +     +  P+ISIKLSALHPRYE +  +RVL EL  T+ +L+  AR L++ I++DAE
Sbjct: 255  ANAKATAGAAAPSISIKLSALHPRYERSQRERVLKELGATLAQLVTRARELDVAITLDAE 314

Query: 308  EVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRL 367
            E DRLELSL+L ++++   A KGWG LG+VVQAYSKRALPVL WLT+LA EQGDEIPVRL
Sbjct: 315  EADRLELSLELLEQVYRQQA-KGWGKLGLVVQAYSKRALPVLHWLTKLAAEQGDEIPVRL 373

Query: 368  VKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQ 427
            VKGAYWD+E+K AQ  G   YP++TRKA TD++YLACARYLL+D  RG ++PQFA+HNA 
Sbjct: 374  VKGAYWDTEIKLAQIEGLPNYPVFTRKANTDIAYLACARYLLADINRGRLFPQFATHNAH 433

Query: 428  TVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAV-RIYAPIGAHKDLLPYLVRRL 486
            T+  +  MAGDR  EFQRLHGMG+ LY   L  A A +  RIYAP+GAHKDLLPYLVRRL
Sbjct: 434  TIICLLAMAGDRPIEFQRLHGMGEALYKQALQLAPAGSYCRIYAPVGAHKDLLPYLVRRL 493

Query: 487  LENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGLN 546
            LENGAN+SFVH+LVD   P+  L  HPL+ L G     N  I LP D++G  R N+KGLN
Sbjct: 494  LENGANSSFVHQLVDEDVPVAQLCRHPLEALAGKANYRNTAIPLPHDLYGPQRPNAKGLN 553

Query: 547  MNIISEAEPFFAALDKFKSTQWQAGPLVNG--QTLTGEHKTVVSPFDTTQTVGQVAFADK 604
            + I S+ EP   A+  +   QWQ GPL+        G  + V SPFD  Q VGQ+ +   
Sbjct: 554  LMINSQLEPLLQAMQPWNQHQWQGGPLLAAAINAAPGPTQAVTSPFDRQQQVGQIQWTSP 613

Query: 605  AAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGID 664
              + QA+ +A  AF  W    V  RA+ L++LADLLE +  EL+ALC REAGK ++DGI 
Sbjct: 614  EQVPQALDAAVLAFPRWNAVAVTERAACLRRLADLLEMHFAELMALCAREAGKQLKDGIA 673

Query: 665  EVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQ 724
            E+REAVDFCRYYA QA++ M +P LLPGPTGE NEL+L G+GVFV ISPWNFP+AIFLGQ
Sbjct: 674  EIREAVDFCRYYADQAEQKMGQPTLLPGPTGESNELYLTGKGVFVAISPWNFPVAIFLGQ 733

Query: 725  VSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERI 784
            +SAA+AAGN V+AKPAEQTS+  +R ++L H+AG+P DVLQ LPG+G  +G  LT+D R+
Sbjct: 734  ISAAVAAGNAVLAKPAEQTSLAAHRCIELMHEAGVPRDVLQLLPGSGKELGPLLTSDPRV 793

Query: 785  GGVCFTGSTGTAKLINRTLANRE-GAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSF 843
             GV FTGSTGTA+ IN  LA RE G +  L+AETGGQNAM+VDST+ PEQVV DV+ SSF
Sbjct: 794  VGVVFTGSTGTAQQINLGLAQRESGPLATLVAETGGQNAMLVDSTALPEQVVADVLESSF 853

Query: 844  TSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDA 903
             SAGQRCSALRVLFLQ+DIAD+V ++L GAM EL +G+P  + TDVGPVIDA A+  L A
Sbjct: 854  ASAGQRCSALRVLFLQDDIADKVEELLAGAMQELKLGDPRELATDVGPVIDAQARGKLQA 913

Query: 904  HIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELA 963
            H++H +Q+G+++ +  +PA    G FV+P A+ +DSI  L  EHFGP+LH++RY ++++ 
Sbjct: 914  HVEHYRQLGRVLAETKVPAAWSQGDFVAPVAIRLDSIDELTSEHFGPVLHIVRYASTDVM 973

Query: 964  HVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSG 1023
             V++ IN +GFGLT GI SRNEG A ++  ++ VGNVYINRN IGAVVGVQPFGG GLSG
Sbjct: 974  QVVESINRSGFGLTFGIQSRNEGFAADIDKRIRVGNVYINRNMIGAVVGVQPFGGMGLSG 1033

Query: 1024 TGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGD 1061
            TGPKAGGPHYL RFVTE+TRT N  AIGGNA+LL+ GD
Sbjct: 1034 TGPKAGGPHYLLRFVTERTRTINTAAIGGNASLLAQGD 1071


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: 2616
Number of extensions: 104
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: 1072
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 1027
Effective search space:  1046513
Effective search space used:  1046513
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: 58 (26.9 bits)

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

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

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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