Alignments for a candidate for rocA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Pseudarthrobacter sulfonivorans Ar51

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_058930844.1 AU252_RS11615 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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



>NCBI__GCF_001484605.1:WP_058930844.1
          Length = 1165

 Score =  247 bits (630), Expect = 5e-69
 Identities = 252/903 (27%), Positives = 393/903 (43%), Gaps = 104/903 (11%)

Query: 147  VGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEAQDEAKEYMAKGYTYSYDML 206
            +G T+  +L +   P+ R V    ++EM    ++     +      +    G   + ++L
Sbjct: 101  LGGTMAPVLPQVVIPIARRV----LREMVGHLIVDATDAKLGPAIAKIRKDGIKLNVNLL 156

Query: 207  GEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRKNPGISVKLSALLARYEYGNKERVMNE 266
            GEA   + +A R        +      ++ DV     +S+K+S+ +A +     +  +  
Sbjct: 157  GEAVLGEHEASRRLAGTHTLL------ARPDVDY---VSIKVSSTVAPHSAWAFDEAVEH 207

Query: 267  LLPRARELVKKAA-----------AANMGF-NIDAEEQDRLDLSLDVIEELVADPELAGW 314
            ++ +   L  KAA           A N  F N+D EE   LD+++ V   ++  PE    
Sbjct: 208  VVEKLTPLFTKAASFAGAASGAGAATNAKFINLDMEEYKDLDMTIAVFTRILDKPEFKNL 267

Query: 315  DGFGVVVQAYGKRSSFVL----DWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVMGLNG 370
            +  G+V+QAY   +   +    DW             VR+VKGA    E   +    L+ 
Sbjct: 268  EA-GIVLQAYLPDALSAMIRLQDWAAERRANGGAAIKVRVVKGANLPMEQVESS---LHD 323

Query: 371  FPVFT--RKACSDVSFLSCATKLLN--MTNRIYPQFATHNAHSVSAILEMAKTKGVDN-Y 425
            +P+ T   K  SD ++       L+    N +    A HN   ++    +AK +GV++  
Sbjct: 324  WPLATWHTKQDSDTNYKRVINYSLHPDRINNVRIGVAGHNLFDIAFAWLLAKQRGVESGI 383

Query: 426  EFQRLHGMGESLHNEVLKVSGVPCRIYAPVGPHKDL---LAYLVRRLLENGANSSFV--- 479
            EF+ L GM +     V K  G    +Y PV    +    +AYL+RRL E  +  +F+   
Sbjct: 384  EFEMLLGMAQGQAEAVKKDVG-SLLLYTPVVHPAEFDVAIAYLIRRLEEGASQDNFMSAV 442

Query: 480  -----NQIVDKRITPEEIAKDPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDP 534
                 NQ++ +R     +A    +  E    N      + P  L  D   N+   D + P
Sbjct: 443  FELSENQVLFEREKQRFLASLDTLDDEVPPANRQQNRSLPPQPLPRDTFANTPDTDPSLP 502

Query: 535  VTVNEIEKGRGAYKDYRWKGGPLIAGEVAGTEIQVVRNPADPDDLVGH--VTQASDADVD 592
                          +  W  G  I   V             P   +G+  V  A+ +D D
Sbjct: 503  A-------------NRTW--GRAILDRV-------------PTSTLGNAAVDAATISDAD 534

Query: 593  TAITSAAAAFE---SWSAKSAEERAACVRKVGDLYEENYAELFALTTREAGKSLLDAVAE 649
            T  T  A A E   +W A + ++RA  + + GD+ E   A+L  +   E GK++     E
Sbjct: 535  TLNTVIATAVEKGKAWGALTGDQRAEILHRAGDVLEARRADLLEVMASETGKTIDQGDPE 594

Query: 650  IREAVDFSQYYANEAIRYKDSGDARGVMCCIS----PWNFPLAIFTGQILANLAAGNTVV 705
            + EAVDF+ YYA  A + +    A  V   ++    PWNFP+AI  G  LA LAAG+ VV
Sbjct: 595  VSEAVDFAHYYAESARKLEKVDGATFVPAKLTVVTPPWNFPVAIPAGSTLAALAAGSAVV 654

Query: 706  AKPAEQTSLLAIRAVELMHQAGIPKDAIQLVPGTGATVGAALTSDSRVSGVCFTGSTATA 765
             KPA+Q        +E + +AG+PKD + +V      +G  L S   V  V  TG   TA
Sbjct: 655  IKPAKQARRSGAVMIEALWEAGVPKDVLTMVQLGERELGQQLISHPSVDRVILTGGYETA 714

Query: 766  QRINKVMTENMAPDAPLVAETGGLNAMIVDSTALPEQVVRDVLASSFQSAGQRCSALRML 825
            +     +  +   D PL+AET G NA+IV  +A  +   +DV  S+F  AGQ+CSA  ++
Sbjct: 715  E-----LFRSFRKDLPLLAETSGKNAIIVTPSADLDLAAKDVAYSAFGHAGQKCSAASLV 769

Query: 826  YVQRDIADG--LLEMLYGAMEELGIGDPWLLSTDVGPVIDENARKKIVDHCEKFERNGKL 883
             +   +A        L  A+  L +G P   ++ +GP+I+    K +       E     
Sbjct: 770  ILVGSVAKSKRFHNQLVDAVTSLKVGYPQDPTSQMGPIIEPADGKLLNALTTLGEGETWA 829

Query: 884  LKKMKVPEKGLFVSPAVLSVSGIEELE----EEIFGPVLHVATFEAKNIDKVVDDINAKG 939
            ++  K+ E G   SP V    G+         E FGPVL V T  A  +++ +   N   
Sbjct: 830  VEPKKLDETGRLWSPGVR--YGVRRGSYFHLTEFFGPVLGVMT--ADTLEEAIAIQNQIE 885

Query: 940  YGLTFGIHSRVDRRVERITSRIKVGNTYVNRNQIGAIVGSQPFGG--EGLSGTGPKAGGP 997
            YGLT G+HS     +      ++ GN YVNR   GAIV  QPFGG  +   G G KAGGP
Sbjct: 886  YGLTAGLHSLNPDELGTWLDSVQAGNLYVNRGITGAIVQRQPFGGWKKSAVGAGTKAGGP 945

Query: 998  QYV 1000
             Y+
Sbjct: 946  NYL 948


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: 2897
Number of extensions: 133
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1209
Length of database: 1165
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1118
Effective search space:  1299116
Effective search space used:  1299116
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 Apr 09 2024. 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