GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Marinobacter guineae M3B

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_099617963.1 CLH62_RS09710 2-hydroxymuconic semialdehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>NCBI__GCF_002744735.1:WP_099617963.1
          Length = 486

 Score =  687 bits (1772), Expect = 0.0
 Identities = 332/462 (71%), Positives = 377/462 (81%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           SP++N VIA + EAG+AEVD AV+AA+ AL G WG++S   RV++LY VAD I RRFDDF
Sbjct: 25  SPVDNQVIASIAEAGQAEVDQAVSAAKHALAGEWGQLSTNDRVDLLYGVADEITRRFDDF 84

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
           +AAE+ DTG+P  +  H  IPRGAANFK+FAD++KNVPTE F M TPDG GA+NY VR P
Sbjct: 85  VAAEMADTGQPHHVMTHAFIPRGAANFKVFADIIKNVPTESFHMDTPDGRGALNYGVRVP 144

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
            GV+GV+ PWN P LLMTWKVGPALACGNTVVVKPSEETP TA LLGEVMN  GVP GVY
Sbjct: 145 KGVIGVVAPWNAPFLLMTWKVGPALACGNTVVVKPSEETPLTATLLGEVMNKVGVPKGVY 204

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263
           NV++GFGP+S GEFLT H DV+AITFTGET TG  IMKAA+DG R VS E+GGKNA IVF
Sbjct: 205 NVINGFGPDSAGEFLTRHKDVDAITFTGETRTGSTIMKAASDGIRDVSFEMGGKNAGIVF 264

Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323
           ADCDLD A++G  RS F N GQVCLGTERVYVERPIFDRFV+ LK+ AEG+  GRP D  
Sbjct: 265 ADCDLDNAVDGIFRSSFLNTGQVCLGTERVYVERPIFDRFVTALKEKAEGVTFGRPTDAG 324

Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383
              GPLISQEHREKVLSYY KA   GAT+VTGGGVP+MP  L  G+WVQPTIWT L + S
Sbjct: 325 VNYGPLISQEHREKVLSYYAKARADGATIVTGGGVPDMPADLAEGSWVQPTIWTDLPESS 384

Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443
            V +EEIFGPC  + PFDSEEEVI  AN +DYGLA  IWT NL+RAHRVAG ++VGI WV
Sbjct: 385 AVIQEEIFGPCCHIRPFDSEEEVIELANASDYGLATTIWTENLTRAHRVAGKVDVGITWV 444

Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485
           NSWFLRDLRTAFGG+KQSGIGREGGVHSLEFYTE++NVCIK+
Sbjct: 445 NSWFLRDLRTAFGGAKQSGIGREGGVHSLEFYTEMRNVCIKM 486


Lambda     K      H
   0.318    0.135    0.406 

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: 737
Number of extensions: 16
Number of successful extensions: 1
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: 485
Length of database: 486
Length adjustment: 34
Effective length of query: 451
Effective length of database: 452
Effective search space:   203852
Effective search space used:   203852
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