GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztC in Pseudomonas putida KT2440

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate PP_1299 PP_1299 putative amino acid ABC transporter - membrane subunit

Query= TCDB::Q52665
         (434 letters)



>lcl|FitnessBrowser__Putida:PP_1299 PP_1299 putative amino acid ABC
           transporter - membrane subunit
          Length = 365

 Score =  300 bits (768), Expect = 5e-86
 Identities = 182/419 (43%), Positives = 236/419 (56%), Gaps = 65/419 (15%)

Query: 16  PAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVWNANSLTECRA 75
           P PV  VG + WMR NLFS  LNT LT+F +   VWL+    P L   + +AN +   RA
Sbjct: 11  PPPVKTVGVLAWMRANLFSSWLNTLLTLFAIYL-VWLI--VPPLLQWALIDANWVGTTRA 67

Query: 76  IIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPRK 135
              +       GACW  ++ R+ QF++G+YP +  WR+ +T     L  AP+     PRK
Sbjct: 68  DCTKE------GACWVFVQQRFGQFMYGYYPTELRWRVDLTVWLAVLGAAPLFIKRFPRK 121

Query: 136 LIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVVAAL 195
                                          A  GL F  L P L   +  G G      
Sbjct: 122 -------------------------------AFYGLGFLVLYPVLAYTLLHG-GY----- 144

Query: 196 FWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQSD 255
                             L L  V + Q+GG +L LVI    IV +LPLGILLALGR+S 
Sbjct: 145 ------------------LGLESVPTSQWGGLMLTLVIATVGIVGALPLGILLALGRRSR 186

Query: 256 MLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFAAAYIA 315
           M  VK + V  IEF RGVPLIT+LF +S++L  FLP G +FD +LR +I V LF +AYIA
Sbjct: 187 MPAVKVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMSFDKLLRAMIGVILFQSAYIA 246

Query: 316 EVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVA 375
           EV+RGGL A+P+GQYEAA A+GL YW++  L+I+PQALK+ IPGIV++FI LFKDT+LV 
Sbjct: 247 EVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVI 306

Query: 376 FVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKRDHR 434
            +GLFD L  +     +D AW G   E Y+F AL+F++F F MSRYSM+LERKL   H+
Sbjct: 307 IIGLFDLLNSVKQAA-ADPAWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHK 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: 621
Number of extensions: 34
Number of successful extensions: 4
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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