GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Pseudomonas stutzeri RCH2

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__psRCH2:GFF3102
          Length = 365

 Score =  285 bits (730), Expect = 1e-81
 Identities = 177/424 (41%), Positives = 235/424 (55%), Gaps = 75/424 (17%)

Query: 16  PAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVWNANSLTECRA 75
           P P   +GA+ W+R NLFS  +NT LT+ GL   +WL+    P L   ++ A+   E RA
Sbjct: 11  PPPTISIGALGWLRANLFSSWINTLLTLVGLYL-LWLI--VPPVLEWAIFKADWTGETRA 67

Query: 76  IIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPRK 135
             +        GACW  I+ R+ QF++GFYP +  WR+                      
Sbjct: 68  DCSRE------GACWVFIQTRFGQFMYGFYPTELRWRVD--------------------- 100

Query: 136 LIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGL--LFTALAPKLGVPVSAGIGLVVA 193
                     AA WL                AI+G   LF    P     +  GIG ++ 
Sbjct: 101 ----------AAAWL----------------AIIGAAPLFLRQMPH---KLRYGIGYLLV 131

Query: 194 ---ALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLAL 250
                +WL               L L  V + Q+GG +L +VI    I  +LPLGILLAL
Sbjct: 132 YPLLAYWLLHGGF----------LGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILLAL 181

Query: 251 GRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFA 310
           GR+SDM  ++ L V  IEF RGVPLIT+LF +S++L  FLP G N D +LR +++V  F 
Sbjct: 182 GRRSDMPAIRVLCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNLDKLLRAMLMVVFFE 241

Query: 311 AAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKD 370
           AAYIAEV+RGGL A+P+GQYEAA A+GL YW++  L+I+PQALK+ IPGIV++FI LFKD
Sbjct: 242 AAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKD 301

Query: 371 TTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLK 430
           T+LV  +GLFD L  I     +D AW G   E Y+F AL++++F F MSRYSM LERKL 
Sbjct: 302 TSLVIIIGLFDFLNSIKRAT-ADPAWLGMSTEGYVFAALVYWMFCFGMSRYSMRLERKLD 360

Query: 431 RDHR 434
             H+
Sbjct: 361 TGHK 364


Lambda     K      H
   0.329    0.143    0.457 

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: 594
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 434
Length of database: 365
Length adjustment: 31
Effective length of query: 403
Effective length of database: 334
Effective search space:   134602
Effective search space used:   134602
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 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