GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pontimonas salivibrio CL-TW6

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_104913734.1 C3B54_RS06275 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_002950575.1:WP_104913734.1
          Length = 488

 Score =  218 bits (555), Expect = 4e-61
 Identities = 145/456 (31%), Positives = 230/456 (50%), Gaps = 19/456 (4%)

Query: 42  PVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEEL 101
           P  G  +  +A C  A+ N AV  A   F +G    L  A+R   L   A  L    +E 
Sbjct: 33  PFTGESVGTIADCGSAEVNSAVAAALRAFKTG----LPRAQRITILEEAARGLDTRRDEF 88

Query: 102 ALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLG-----LVTRE 156
           A +  L+ GK + D  + ++  A + + +TA         V P    + G     +  R 
Sbjct: 89  AAVIALETGKSLKDCRT-EVARATETLRYTAAEARTQSSRVIPADAAEAGEGALAMEMRV 147

Query: 157 PVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGV 216
           P GVVGAI P+NFPL  +  K+ PALA G SVV KP+ ++PLTA+ +  L  EAG+ AG 
Sbjct: 148 PRGVVGAITPFNFPLNTSVHKVAPALAVGCSVVHKPAHQTPLTALALQDLFREAGLGAGW 207

Query: 217 LNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIV 276
           L V    G   G+AL  H DV  + FTGS  +  ++   A ++  K++ LE G  +P ++
Sbjct: 208 LEVCTDGGGNAGRALVEHSDVAVISFTGSNVVGWEI---AQKAPKKKVLLELGSNAP-VI 263

Query: 277 FADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLD 336
             +  DL  AA+  A+    + G+ C +  R++  +SI  K    +       + G+P D
Sbjct: 264 VTETADLAHAAKRIATGGFGSAGQSCISVQRVIAHQSIASKLEDHLAAVAGEIQAGDPFD 323

Query: 337 PQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMR 396
           P+  +G L+  +  + V  +++   + G  ++              + P I  G     R
Sbjct: 324 PKVDIGPLISLEASSRVREWVQEAVEMGGAIVG----NTPNNDSVAIAPIIISGAPEKSR 379

Query: 397 IAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVN 456
           I Q+EIFGPV++V+ ++T +EA+AIANDT +GL AG++TSD+S+       +  G V +N
Sbjct: 380 IRQKEIFGPVITVLPYNTFDEALAIANDTIFGLQAGVFTSDVSEMLSAFHQLEFGGVLIN 439

Query: 457 QYDGGDMT-APFGGFKQSGNGRDKSLHALEKYTELK 491
                 +   P+GG  +SGN R+   +A+E+ T L+
Sbjct: 440 DIPTVRLDHQPYGGVAESGNTREGPHYAMEELTHLR 475


Lambda     K      H
   0.316    0.132    0.390 

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: 581
Number of extensions: 32
Number of successful extensions: 4
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: 497
Length of database: 488
Length adjustment: 34
Effective length of query: 463
Effective length of database: 454
Effective search space:   210202
Effective search space used:   210202
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: 52 (24.6 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