GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Pseudomonas fluorescens FW300-N2E2

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Pf6N2E2_5404 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5404
          Length = 365

 Score =  298 bits (764), Expect = 1e-85
 Identities = 175/420 (41%), Positives = 235/420 (55%), Gaps = 67/420 (15%)

Query: 16  PAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPW-LLHGVWNANSLTECR 74
           P P S +G + WMR N+FS  +NT LT+F       +V     W +L   W   +  +C 
Sbjct: 11  PPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRADCT 70

Query: 75  AIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDALPR 134
                       GACW  I+ R+ QF++G+YP D  WR+ +T     + +AP+     PR
Sbjct: 71  K----------EGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPR 120

Query: 135 KLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVVAA 194
           K                               AI GL F  L      P+SA   L+   
Sbjct: 121 K-------------------------------AIYGLSFLVL-----YPISAWC-LLHGG 143

Query: 195 LFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQS 254
           +F L A A                  + Q+GG +L LVI    IV +LPLGI+LALGR+S
Sbjct: 144 VFGLDAVA------------------TSQWGGLMLTLVIATVGIVGALPLGIVLALGRRS 185

Query: 255 DMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFAAAYI 314
           +M  ++ + V  IEF RGVPLIT+LF +S++L  FLP G NFD +LR +I V LF +AYI
Sbjct: 186 NMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYI 245

Query: 315 AEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLV 374
           AEV+RGGL A+P+GQYEAA A+GL YW++  L+I+PQALK+ IPGIV++FI LFKDT+LV
Sbjct: 246 AEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLV 305

Query: 375 AFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKRDHR 434
             +GLFD L  +     +D  W G   E Y+F AL+F++F F MSRYSM+LERKL   H+
Sbjct: 306 IIIGLFDLLNSVKQAA-ADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHK 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: 613
Number of extensions: 25
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:

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