GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Pseudovibrio axinellae Ad2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_068010021.1 PsAD2_RS20095 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::Marino:GFF2744
         (1209 letters)



>NCBI__GCF_001623255.1:WP_068010021.1
          Length = 1212

 Score = 1353 bits (3503), Expect = 0.0
 Identities = 695/1210 (57%), Positives = 871/1210 (71%), Gaps = 12/1210 (0%)

Query: 8    TPELVDSRQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIM 67
            TPE++  R  IRD YL DE +V+ E+I+  Q+ +A R+  S  AA+L++ +R N   TIM
Sbjct: 6    TPEII--RDKIRDNYLPDEKQVVQELISSLQMDEAARERASRGAADLIQDLRANTSPTIM 63

Query: 68   EKFLAEYGLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINT 127
            E FL EYGL+T+EG+ALMCLAEALLRVPD  TI  LI DKIT  AWG H+G++SS LIN 
Sbjct: 64   ESFLGEYGLSTQEGIALMCLAEALLRVPDAQTIDALIADKITPSAWGEHLGRSSSTLINA 123

Query: 128  ATVALLMTSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEA 187
            +T ALL+T  +L   ++  VG T+R ++KR GEPV+RT   QAMKE+GRQFVLGR I EA
Sbjct: 124  STWALLLTGKVLAPDDQGLVG-TIRGVVKRMGEPVVRTAVAQAMKELGRQFVLGRTIREA 182

Query: 188  QDEAKEYMAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKG-DVRKNPGISV 246
               A+     G+TYSYDMLGEAA TD DAKRY+ SYS AI +++   K   +R+NPGISV
Sbjct: 183  MRNARVEEGNGFTYSYDMLGEAACTDADAKRYHLSYSKAITALSSNCKHHSIRENPGISV 242

Query: 247  KLSALLARYEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELV 306
            KLSAL  RYE+  +ERVM EL+PR   L+  A ++NMGFNIDAEE DRLD+SLDVIE L+
Sbjct: 243  KLSALHPRYEFAKRERVMKELVPRTLSLIMLAKSSNMGFNIDAEEADRLDISLDVIEALL 302

Query: 307  ADPELAGWDGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVM 366
            ADP   GWDGFGVVVQA+G R++ V+DWLY +A+KYDRK MVRLVKGAYWD EIKRAQ +
Sbjct: 303  ADPATEGWDGFGVVVQAFGPRATHVIDWLYAVAQKYDRKIMVRLVKGAYWDTEIKRAQTL 362

Query: 367  GLNGFPVFTRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYE 426
            G+ G+PVFTRK  +D+SF  CA KLL MT+RIYPQFATHNAHSV+ ILE+AK   +++YE
Sbjct: 363  GIEGYPVFTRKVSTDLSFTVCAEKLLAMTDRIYPQFATHNAHSVATILELAKNLPLNSYE 422

Query: 427  FQRLHGMGESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKR 486
            FQRLHGMGE+LH   +K  G  CRIYAPVG HKDLLAYLVRRLLENGANSSFV+QI D+ 
Sbjct: 423  FQRLHGMGEALHERTMKKHGSNCRIYAPVGAHKDLLAYLVRRLLENGANSSFVHQIRDES 482

Query: 487  ITPEEIAKDPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGA 546
            ++P+ IA+DP++ +E  G  IS+  I  P  L+G  R+N+KGWD+TDP    +  +   +
Sbjct: 483  VSPKAIAQDPLMHIEAYGEQISNAKIALPPALYGSGRKNAKGWDLTDPKQETQYVESMKS 542

Query: 547  YKDYRWKGGPLIAGEVAGTEIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWS 606
            +   +W+G P+IA  V       V+NPAD  D VGHV  A+   ++ A+T+A A  + W+
Sbjct: 543  FLTTKWEGHPVIAASVKNATAIAVKNPADLRDTVGHVATATPEQIEAALTAAHAGCKEWT 602

Query: 607  AKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIR 666
             K+A++RA  +RK  DL EEN +E+FAL TREAGK+ +DA+ E+REAVDF +YYANEAIR
Sbjct: 603  EKNAQDRAVVLRKAADLLEENASEIFALLTREAGKTYMDAINELREAVDFGRYYANEAIR 662

Query: 667  YKD---SGDARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELM 723
             ++     DARG + CISPWNFPLAIF+GQI A LAAGN V+AKPA QT L+A  AV LM
Sbjct: 663  LEERDGKSDARGPVTCISPWNFPLAIFSGQIFAALAAGNPVLAKPAPQTPLIATYAVGLM 722

Query: 724  HQAGIPKDAIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLV 783
            HQAGIP  A+QL+PG G  VGAALTSD RV+GVCFTGSTATAQ IN+ M   + P APL+
Sbjct: 723  HQAGIPVQALQLLPGAG-EVGAALTSDKRVAGVCFTGSTATAQHINRAMANALCPTAPLI 781

Query: 784  AETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAM 843
            AETGGLNAMIVDSTALPEQ VRDV+ASSFQSAGQRCSALRMLYVQ DI +   EML GAM
Sbjct: 782  AETGGLNAMIVDSTALPEQAVRDVIASSFQSAGQRCSALRMLYVQEDIFEDFKEMLLGAM 841

Query: 844  EELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSV 903
             EL +GDP  LSTDVGPVID  A+ KI  HC+K+   G++LK++K P KG FV+P ++ +
Sbjct: 842  AELELGDPSALSTDVGPVIDAAAQSKIDAHCKKWAEKGRVLKQLKAPNKGHFVAPTLIHL 901

Query: 904  SGIEELEEEIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKV 963
             GIEEL EEIFGPVLH+ATF+A+ ID+ +D IN +GYGLTFG+H+RVD RV+ +  R+KV
Sbjct: 902  DGIEELGEEIFGPVLHIATFKAEEIDQTIDAINGQGYGLTFGLHTRVDSRVQHVVERVKV 961

Query: 964  GNTYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLKGETVEREADSNARKVDAK 1023
            GN YVNRNQIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF + +T   E+ +  +   A+
Sbjct: 962  GNLYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPHYLSRFARADTKSAESVTLHKSFTAE 1021

Query: 1024 QLQKLIGQLDKLKASRPEARMDAIRPIFGNVPEPLDAHVEA----LPGPTGETNRLSNHA 1079
             + K  G +         AR   +  +F      L    +     +PGPTGE+NRL +  
Sbjct: 1022 DIFKAHGAVRTNNWESNSARFTELATLFKQEAHLLHRAAQEQAYDMPGPTGESNRLYSAP 1081

Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139
            RG VLCLGPD E+   Q   AL+ GN V+ +  G + +         PIV  +G L    
Sbjct: 1082 RGTVLCLGPDTESLKHQVVLALAAGNSVIAVGQGAEKLAASLRSFSAPIVALEGQLAEGT 1141

Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199
            L  + G +A+ +   +  LK  +  LA RDGAL+ LI E    +R+ +ERHLC+DTTA+G
Sbjct: 1142 LTKLQGIDAIAANHSEEDLKVMKGELADRDGALMQLIMERNQIERYQLERHLCIDTTASG 1201

Query: 1200 GNASLIAASE 1209
            GN SL+AASE
Sbjct: 1202 GNTSLLAASE 1211


Lambda     K      H
   0.316    0.133    0.378 

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: 3313
Number of extensions: 142
Number of successful extensions: 7
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: 1209
Length of database: 1212
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1165
Effective search space:  1353730
Effective search space used:  1353730
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: 59 (27.3 bits)

This GapMind analysis is from Sep 24 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