GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Rhodobacter viridis JA737

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_110805920.1 C8J30_RS10945 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= curated2:Q2G9T9
         (471 letters)



>NCBI__GCF_003217355.1:WP_110805920.1
          Length = 1127

 Score =  198 bits (503), Expect = 9e-55
 Identities = 160/457 (35%), Positives = 222/457 (48%), Gaps = 39/457 (8%)

Query: 11  PATGAEVWRGKVGDVEEVVAR--ARRAWPAWAAQPLATRIELVRRFANEVRKDADNLATM 68
           PATGA V R    D   V     A R W A    P A R  ++ R A+   ++   +   
Sbjct: 553 PATGAVVARVTEADAATVAVALDAARVWSA----PAAERAAVLSRAADLYEENFGPIFAA 608

Query: 69  ISRETGKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAALRHKPHGVLAVL 128
           ++RE GK L +A +E+   V+     +R YA            +GT+  R  P G +  +
Sbjct: 609 LAREAGKTLGDAISELREAVD----FLRYYA-----------AEGTSDTR-APRGPVVAI 652

Query: 129 GPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGIPAAVVQVLIG-G 187
            P+NFP  +  G I  AL+AGNAV+ KP+E+TP    +  +  H+AG+PA  +Q+L G G
Sbjct: 653 SPWNFPLAIFTGQIAAALMAGNAVLAKPAEQTPVIAALAVRLLHQAGVPATALQLLPGDG 712

Query: 188 PEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASN--PGKIVALEMGGNNPIVVWDTPKI 245
           P  G AL     I GV+FTGS      I R +A++  PG  +  E GG N +VV  T   
Sbjct: 713 PTVGAALTRDPRIKGVVFTGSTETAQIIARAMAAHMAPGTPLIAETGGLNAMVVDSTALP 772

Query: 246 EDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGAPFDDPAPFMG 305
           E A   +V SAF SAGQRC+A R L ++  +   VI  +K   D +++G P+   +  +G
Sbjct: 773 EQAVRDVVASAFRSAGQRCSALRCLYVQEDIAPHVIAMLKGAMDELVLGDPW-RLSTDVG 831

Query: 306 PVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAVADRPDVELFGP 365
           PVID     G+     YL  + GR I H         F++PA++ VT +AD    E+FGP
Sbjct: 832 PVIDAEAQAGIE---TYLAQNAGR-ILHRTAAPAGGHFVAPALLKVTGIADLSH-EIFGP 886

Query: 366 LLQVV--RVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVVNWNRPTNGA- 422
           +L +     DD    IA  N   +GL+  L              IRAG +  NR   GA 
Sbjct: 887 VLHLATFAADDLPAVIAAINARGYGLTFGLHSRIDARVETVAETIRAGNIYVNRNQIGAV 946

Query: 423 SSAAPFGGVGLSGNHRPSA----YYAADYCAYPVAST 455
             + PFGG GLSG   P A    Y    Y   PV +T
Sbjct: 947 VGSQPFGGEGLSGT-GPKAGGPLYLGRFYAPEPVVAT 982


Lambda     K      H
   0.319    0.135    0.403 

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: 1253
Number of extensions: 71
Number of successful extensions: 6
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: 471
Length of database: 1127
Length adjustment: 40
Effective length of query: 431
Effective length of database: 1087
Effective search space:   468497
Effective search space used:   468497
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

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

Links

Downloads

Related tools

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