Alignments for a candidate for put1 in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Rhodobacter viridis JA737

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_110805920.1 C8J30_RS10945 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::Phaeo:GFF1160
         (1158 letters)



>NCBI__GCF_003217355.1:WP_110805920.1
          Length = 1127

 Score = 1274 bits (3297), Expect = 0.0
 Identities = 692/1130 (61%), Positives = 818/1130 (72%), Gaps = 21/1130 (1%)

Query: 33   YVDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAEYGLSTDEGV 92
            +  +A++ + L A A L       I+A  A LV  IR  + P LME FLA+YGLST EGV
Sbjct: 13   FAPEAEVLEALVAQAALPQAQLDRIAARGADLVARIRAEAKPSLMEHFLAQYGLSTREGV 72

Query: 93   ALMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALMLTGKVLDEK 152
            ALMCLAEA+LRVPD  TIDALIEDKIAPS+WGKHLG + SSLVNASTWALMLTGKVLD+ 
Sbjct: 73   ALMCLAEAMLRVPDNATIDALIEDKIAPSDWGKHLGTAASSLVNASTWALMLTGKVLDDG 132

Query: 153  RSPVSA-LRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGMEAKGYTYSY 211
               ++  LRGAM+RLGEPVIR AV +AM+EMGRQFVLGETIE A++RA   E++GYT+SY
Sbjct: 133  AGGLAGTLRGAMRRLGEPVIRAAVGQAMREMGRQFVLGETIEKALERAEKRESEGYTFSY 192

Query: 212  DMLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHPRYELAQETS 271
            DMLGEAA T ADA RY +AY++AI++IA A     I  NPGIS+KLSALHPRYE+AQE  
Sbjct: 193  DMLGEAALTTADAERYRVAYAQAIASIAKAATKGSIAANPGISIKLSALHPRYEVAQEAR 252

Query: 272  VKEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAGWDGFGVVVQ 331
            V  +LVP ++ LA  A AAG+ L++DAEE DRL+LSL VIE V++DP  AGW GFG VVQ
Sbjct: 253  VMAELVPVVRDLARAAAAAGIALHIDAEEQDRLALSLRVIEAVMADPETAGWQGFGAVVQ 312

Query: 332  AYGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPVFTHKSLTDV 391
            AYG R GAA+DAL  MA    RR+ +RLVKGAYWD+E+KRAQVEG  GFP+FT K+ TDV
Sbjct: 313  AYGKRAGAAIDALAAMARASGRRINIRLVKGAYWDSEMKRAQVEGHPGFPLFTSKTGTDV 372

Query: 392  SYIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGMGETLHNMVL 451
            +YI  A KL  ++D +YPQFATHNAHTV+A+L MA       YEFQRLHGMG  LH++VL
Sbjct: 373  AYICLAAKLFGLSDCLYPQFATHNAHTVAAVLEMAAGR---PYEFQRLHGMGARLHDIVL 429

Query: 452  EQNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVAADPFAQVED 511
             +    CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIV+E+VPP  VAA PFA +  
Sbjct: 430  RETGGRCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVNESVPPSEVAACPFAALAT 489

Query: 512  LTA--NLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLLAKAPETA 569
              A   L     LF  +R NS GFDL     LA I+ AR         A P++A  P + 
Sbjct: 490  ARAPRGLLAPAALFGSDRVNSQGFDLSDPEVLARIETARTVTLPD---AAPIVA-GPVSG 545

Query: 570  TTTDEPVRNPADLTTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAADLYEANYG 629
             + D  V NPA    V RV  A  A +  AL AA  W+A A  RA VL+RAADLYE N+G
Sbjct: 546  GSRD--VVNPATGAVVARVTEADAATVAVALDAARVWSAPAAERAAVLSRAADLYEENFG 603

Query: 630  ELFALLTREAGKTLPDCVAELREAVDFLRYYAARISAE--PPVGVFTCISPWNFPLAIFS 687
             +FA L REAGKTL D ++ELREAVDFLRYYAA  +++   P G    ISPWNFPLAIF+
Sbjct: 604  PIFAALAREAGKTLGDAISELREAVDFLRYYAAEGTSDTRAPRGPVVAISPWNFPLAIFT 663

Query: 688  GQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAG-AVGGALTSDA 746
            GQIAAAL  GNAVLAKPAEQTP+IA  A+ LLH+AGVP +ALQLLPG G  VG ALT D 
Sbjct: 664  GQIAAALMAGNAVLAKPAEQTPVIAALAVRLLHQAGVPATALQLLPGDGPTVGAALTRDP 723

Query: 747  RVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQSIIESA 806
            R+ GV FTGST TA  I  AMA H+ PG PLIAETGGLNAM+VDSTALPEQAV+ ++ SA
Sbjct: 724  RIKGVVFTGSTETAQIIARAMAAHMAPGTPLIAETGGLNAMVVDSTALPEQAVRDVVASA 783

Query: 807  FQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETARAGIL 866
            F+SAGQRCSALRCLY+QEDIA +V+ MLKGAMD L LGDPW LSTD GPVID  A+AGI 
Sbjct: 784  FRSAGQRCSALRCLYVQEDIAPHVIAMLKGAMDELVLGDPWRLSTDVGPVIDAEAQAGIE 843

Query: 867  AHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQDLDQI 926
             ++  A+  GR+L    AP GG FVAP L+++TGI  L  EIFGPVLH+  F + DL  +
Sbjct: 844  TYL--AQNAGRILHRTAAPAGGHFVAPALLKVTGIADLSHEIFGPVLHLATFAADDLPAV 901

Query: 927  IRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEGLSGTG 986
            I  INA GYGLTFGLH+RID RV+ + + I AGN+YVNRNQIGA+VGSQPFGGEGLSGTG
Sbjct: 902  IAAINARGYGLTFGLHSRIDARVETVAETIRAGNIYVNRNQIGAVVGSQPFGGEGLSGTG 961

Query: 987  PKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTMLPAPTGQPMQEITTSLPGPTGESNRLS 1046
            PKAGGP Y+ RF AP+   +  +W        +LP      + E+   LPGPTGE NRL+
Sbjct: 962  PKAGGPLYLGRFYAPEPVVATGAWTQ--AVTPVLPEAVETLLGEL--FLPGPTGELNRLT 1017

Query: 1047 QLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTSGVIWWGDETT 1106
            +  R P+LCLGPGP+A  AQA AV  LGG A++ATG +  + L T E  + V+WWG+   
Sbjct: 1018 RHVRGPVLCLGPGPEAAAAQAAAVAVLGGQAVQATGAVAAKALGTAEPLAAVLWWGEAEM 1077

Query: 1107 AREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALLGG 1156
             R     LA R GP++PLI   PD A V  ERH+CVDTTAAGGNAALL G
Sbjct: 1078 GRAYAQALAARPGPLVPLITARPDLAHVAHERHLCVDTTAAGGNAALLAG 1127


Lambda     K      H
   0.317    0.132    0.387 

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: 3133
Number of extensions: 128
Number of successful extensions: 9
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: 1158
Length of database: 1127
Length adjustment: 46
Effective length of query: 1112
Effective length of database: 1081
Effective search space:  1202072
Effective search space used:  1202072
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: 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