GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Cupriavidus basilensis 4G11

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate RR42_RS32650 RR42_RS32650 betaine-aldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__Cup4G11:RR42_RS32650
          Length = 484

 Score =  736 bits (1899), Expect = 0.0
 Identities = 351/462 (75%), Positives = 399/462 (86%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           +P++N++IA+VHEAG+AEVDAAVAAA+ AL+G WG+M++A+RVE+L+AVADGINRRFDDF
Sbjct: 23  NPVDNSLIARVHEAGQAEVDAAVAAAKQALRGPWGKMTVARRVEILHAVADGINRRFDDF 82

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
           L AE+ DTGKP SLA HVDIPRGAANFK+FAD++KNVPTE F M TPDG  AINYAVR P
Sbjct: 83  LQAEIADTGKPHSLASHVDIPRGAANFKVFADLIKNVPTESFAMATPDGGEAINYAVRSP 142

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
            GV+GV+CPWNLPLLLMTWKVGPALACGNTVVVKPSEETP TA LLGEVMN AGVPPGVY
Sbjct: 143 RGVIGVVCPWNLPLLLMTWKVGPALACGNTVVVKPSEETPATATLLGEVMNEAGVPPGVY 202

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263
           NVVHGFGP+S G FLT+HPDVN ITFTGET TGEAIMKAAA+G RPVS ELGGKNA IVF
Sbjct: 203 NVVHGFGPDSAGAFLTAHPDVNGITFTGETRTGEAIMKAAANGVRPVSFELGGKNAGIVF 262

Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323
           AD D DKA+ G  RS F N GQVCLGTERVYV+RPIF RFV+ LK  AE +++GRP D  
Sbjct: 263 ADADFDKAVAGITRSAFENSGQVCLGTERVYVQRPIFARFVAALKARAEALRIGRPNDEG 322

Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383
             MGPL+S EHR+KVLSYY+KA +AGATVVTGGGVPEMP AL  GAWVQPTIWTGL +D+
Sbjct: 323 VNMGPLVSLEHRDKVLSYYRKAADAGATVVTGGGVPEMPGALAEGAWVQPTIWTGLPEDA 382

Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443
            V REEIFGPC  + PFD+EEE IR AND  YGLA  +WT++L  AHR+  A+EVGI W+
Sbjct: 383 AVIREEIFGPCCHIAPFDTEEEAIRLANDTPYGLAATVWTSDLGTAHRMGSALEVGICWI 442

Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485
           N+WFLRDLRTAFGG+KQSGIGREGGVHSLEFYTEL+NVC+KL
Sbjct: 443 NAWFLRDLRTAFGGAKQSGIGREGGVHSLEFYTELRNVCVKL 484


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: 728
Number of extensions: 17
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: 484
Length adjustment: 34
Effective length of query: 451
Effective length of database: 450
Effective search space:   202950
Effective search space used:   202950
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 17 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