GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Bacteroides thetaiotaomicron VPI-5482

Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate 351599 BT2071 isocitrate dehydrogenase [NADP] (NCBI ptt file)

Query= BRENDA::Q4J6C9
         (411 letters)



>FitnessBrowser__Btheta:351599
          Length = 396

 Score =  347 bits (891), Expect = e-100
 Identities = 178/394 (45%), Positives = 255/394 (64%), Gaps = 17/394 (4%)

Query: 19  GKWVVPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLEVYAGEKANKIT 78
           G   VP+ P++ YI GDG+G E+T S   VVN AV+KAY   R I+W EV AGE+A   T
Sbjct: 10  GTLSVPDVPVVPYITGDGVGAEVTPSMQSVVNAAVQKAYGGKRRIEWKEVLAGERAFNET 69

Query: 79  GDRFPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYANIRPVKYIEGLESP 138
           G   P ET     +Y + +KGPL TP+G G +S+NVA+R  LDLY  +RPV++ +G+ SP
Sbjct: 70  GSWLPDETMKAFQEYLIGIKGPLTTPVGGGIRSLNVALRQTLDLYVCLRPVRWYQGVHSP 129

Query: 139 LKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREEL---KVDIEDDTGIGLKV 195
           +K PEKV+M +FRENT+D+Y GIE+   + EA+K  +FL+ E+   KV   + +  G+K 
Sbjct: 130 VKAPEKVNMCVFRENTEDIYAGIEWEAGTPEAEKFYQFLKNEMGVTKVRFPETSSFGVKP 189

Query: 196 MSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYEVALNEYRDKIVTE 255
           +S+  T+R+ R A  YAL +    VT++HKGN+MK+TEG F++W YE+A  E+ D +   
Sbjct: 190 VSREGTERLVRAACQYALDHHLPSVTLVHKGNIMKFTEGGFKKWGYELAQREFGDAL--- 246

Query: 256 EEINRGVNSEGKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGM 315
                   ++G++++ D IAD  LQ  ++ P+EY +I   N+NGDY+SD   A++G IG+
Sbjct: 247 --------ADGRLVIKDCIADAFLQNTLLIPEEYSVIATLNLNGDYVSDQLAAMVGGIGI 298

Query: 316 LGGANIGDTGG--MFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEAARLIEKAI 373
             GANI    G  +FEA HGTAP  AGK+V NP  II S  +ML ++GW EAA LIEKA+
Sbjct: 299 APGANINYKTGHAIFEATHGTAPNIAGKDVVNPCSIILSAVMMLEYLGWKEAAALIEKAL 358

Query: 374 NESIKQKKVTQDIARYL-GITPLGTKEYTDTLVQ 406
            +S    + T D+AR++ G T L T  +T  +V+
Sbjct: 359 EQSFLDARATHDLARFMPGGTSLSTTAFTREIVE 392


Lambda     K      H
   0.317    0.137    0.394 

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: 425
Number of extensions: 18
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: 411
Length of database: 396
Length adjustment: 31
Effective length of query: 380
Effective length of database: 365
Effective search space:   138700
Effective search space used:   138700
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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