GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Lutibaculum baratangense AMV1

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_023434135.1 N177_RS19425 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_000496075.1:WP_023434135.1
          Length = 489

 Score =  654 bits (1686), Expect = 0.0
 Identities = 316/482 (65%), Positives = 393/482 (81%), Gaps = 3/482 (0%)

Query: 2   QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61
           +LKDA L + Q YV+G WV       I V NPATGE + SVP+ G AE R AIEAA+KA 
Sbjct: 9   RLKDASLLKSQCYVNGRWVGEGE---IAVTNPATGETLASVPRFGGAEAREAIEAAEKAF 65

Query: 62  PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121
             W   TAKER+  LRRW++LM+EN++DLA +MT EQGKPL E++GEI YAA+F+E+F E
Sbjct: 66  KPWAKKTAKERSKILRRWYELMMENKEDLAFIMTSEQGKPLTESRGEIDYAANFVEFFAE 125

Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181
           EAKRIYGDTIP H+ D RI+V KQPIGVT AITPWNFP+AMITRKAGPALAAGCTMV+KP
Sbjct: 126 EAKRIYGDTIPSHKADARIVVGKQPIGVTCAITPWNFPAAMITRKAGPALAAGCTMVVKP 185

Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQL 241
           A++TP +ALALAELA RAGIP+GVFSV+TG + E+G E+TSNPIV+ +TFTGSTE+G++L
Sbjct: 186 ATETPLTALALAELAHRAGIPEGVFSVITGKSSEIGAEMTSNPIVKLITFTGSTEVGKKL 245

Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301
           M + A  +KKV+LELGGNAPF+VFDDADLDAAV+GA+ SK+RN GQTCVCANR+YVQ GV
Sbjct: 246 MEQSASTVKKVALELGGNAPFLVFDDADLDAAVQGAIASKFRNMGQTCVCANRIYVQSGV 305

Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361
           Y+AF  KL  AV KL +G+G +  V  GPLI+  AV KVEEHI+DA SKGAKVV GGK  
Sbjct: 306 YEAFAGKLAEAVKKLKVGDGAQEDVQQGPLINEDAVKKVEEHISDATSKGAKVVLGGKRS 365

Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421
            LG +FF+PT+L DV    +V+++ETFGP+AP+FRF+ E E I ++N T+FGLASYFY+R
Sbjct: 366 DLGHSFFQPTVLTDVTPEMVVTREETFGPVAPLFRFETEEEAIELANATQFGLASYFYSR 425

Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481
           D+ R +RVAE LEYG+VGIN GLIS EVAPFGG+K SG+GREGS YG+++++E+KY+ +G
Sbjct: 426 DIGRCWRVAEALEYGIVGINEGLISTEVAPFGGVKESGIGREGSHYGMDEFVEVKYMLMG 485

Query: 482 GI 483
           G+
Sbjct: 486 GL 487


Lambda     K      H
   0.317    0.135    0.391 

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: 681
Number of extensions: 9
Number of successful extensions: 2
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: 483
Length of database: 489
Length adjustment: 34
Effective length of query: 449
Effective length of database: 455
Effective search space:   204295
Effective search space used:   204295
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: 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