GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Pseudomonas fluorescens GW456-L13

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate PfGW456L13_1700 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1700
          Length = 365

 Score =  249 bits (635), Expect = 1e-70
 Identities = 144/379 (37%), Positives = 222/379 (58%), Gaps = 40/379 (10%)

Query: 4   LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63
           + W+R N+FS+W N+LLT+    L   +V  I+       QWA++  N            
Sbjct: 20  MAWMRANMFSSWLNTLLTLFAFYLIYLVVPPIL-------QWAILDAN------------ 60

Query: 64  EYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWLLL 123
                W+  + A         +F  Q      + G F +     ++ + +DL+  +WL +
Sbjct: 61  -----WVGTSQADCTKEGACWVFIQQ------RFGQFMYGYYPPVLRWRVDLT--VWLAI 107

Query: 124 TAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLRPVSSNLWNGLLLT 181
             V   P F+  SR  +     LS  +L+ +PII W +  GG  GL  V+++ W GL+LT
Sbjct: 108 VGVA--PLFI--SRFHHKAVYGLS--FLVLYPIIAWCLLHGGVLGLDAVATSQWGGLMLT 161

Query: 182 LLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPLFF 241
           L++A + I  + P+G++LALGR SN+P +R   + +IE  RGVPLI +LF++ VMLPLF 
Sbjct: 162 LVIATVGIAGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFL 221

Query: 242 AADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIVLP 301
              +  D++LRA+ G++LF +AY+AE VRGGLQA+ +GQ EAA A+GL  +  + L++LP
Sbjct: 222 PEGMNFDKLLRALIGVILFQSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILP 281

Query: 302 QALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGLIY 361
           QAL+ VIP +V  FI LFKDTSL+ ++GL +L    +   A P+++G   E Y+F  L++
Sbjct: 282 QALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVF 341

Query: 362 WLFCYSMSLASRRLERQLN 380
           W+FC+ MS  S  LER+L+
Sbjct: 342 WIFCFGMSRYSMHLERKLD 360


Lambda     K      H
   0.332    0.145    0.452 

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: 489
Number of extensions: 23
Number of successful extensions: 3
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: 381
Length of database: 365
Length adjustment: 30
Effective length of query: 351
Effective length of database: 335
Effective search space:   117585
Effective search space used:   117585
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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